##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MACPET.buildbin-libdir && mkdir MACPET.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MACPET.buildbin-libdir MACPET_1.12.0.tar.gz
###
##############################################################################
##############################################################################



install for i386

* installing *source* package 'MACPET' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Stage_0_FastqFilteringSubFunctions.cpp -o Stage_0_FastqFilteringSubFunctions.o
Stage_0_FastqFilteringSubFunctions.cpp: In function 'SEXPREC* FilterFastqYield_fun_Rcpp(int&, std::vector<std::__cxx11::basic_string<char> >&, Rcpp::NumericVector&, std::vector<std::__cxx11::basic_string<char> >&, Rcpp::NumericVector&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&)':
Stage_0_FastqFilteringSubFunctions.cpp:55:36: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
         if(SreadFastq1[i].find(NNs)!=-1||SreadFastq2[i].find(NNs)!=-1){
            ~~~~~~~~~~~~~~~~~~~~~~~~^~~~
Stage_0_FastqFilteringSubFunctions.cpp:55:66: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
         if(SreadFastq1[i].find(NNs)!=-1||SreadFastq2[i].find(NNs)!=-1){
                                          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Stage_3_PeakFinderSubFunctions.cpp -o Stage_3_PeakFinderSubFunctions.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:187,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_3_PeakFinderSubFunctions.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h: In function 'Rcpp::List PrepLocFit_Rcpp(Rcpp::DataFrame&, const DataFrame&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h:442:13: warning: 'ChromSize' may be used uninitialized in this function [-Wmaybe-uninitialized]
             r_vector_start<RTYPE>(x)[0] = object;
             ^~~~~~~~~~~~~~
Stage_3_PeakFinderSubFunctions.cpp:61:9: note: 'ChromSize' was declared here
     int ChromSize;//initiate to find them.
         ^~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Stage_4_InteractionsSubFunctions.cpp -o Stage_4_InteractionsSubFunctions.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw32/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
Stage_4_InteractionsSubFunctions.cpp: In function 'SEXPREC* Get_NewPeakSummit_fun_Rcpp(const NumericVector&, const NumericVector&, const NumericVector&, const NumericVector&, const int&, const int&)':
Stage_4_InteractionsSubFunctions.cpp:47:39: warning: 'PeakSummit_opt' may be used uninitialized in this function [-Wmaybe-uninitialized]
         PeakSummitNew[MergedPeakCount]=PeakSummit_opt;
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o MACPET.dll tmp.def RcppExports.o Stage_0_FastqFilteringSubFunctions.o Stage_3_PeakFinderSubFunctions.o Stage_4_InteractionsSubFunctions.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/MACPET.buildbin-libdir/00LOCK-MACPET/00new/MACPET/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MACPET'
    finding HTML links ... done
    AnalysisStatistics                      html  
    ConvertToPE_BAM                         html  
    ConvertToPSelf                          html  
    GenomeMap-class                         html  
    GetShortestPath                         html  
    GetSignInteractions                     html  
    MACPET                                  html  
    finding level-2 HTML links ... done

    MACPETUlt                               html  
    MACPET_GenomeMapData.rda                html  
    MACPET_pinterData.rda                   html  
    MACPET_pintraData.rda                   html  
    MACPET_pselfData.rda                    html  
    MACPET_psfitData.rda                    html  
    PInter-class                            html  
    PIntra-class                            html  
    PSFit-class                             html  
    PSelf-class                             html  
    PeaksToGRanges                          html  
    PeaksToNarrowPeak                       html  
    SampleChIAPETData.bam                   html  
    SampleChIAPETDataRead_1.bam             html  
    SampleChIAPETDataRead_2.bam             html  
    TagsToGInteractions                     html  
    exportPeaks                             html  
    plot                                    html  
    summary                                 html  
** 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

install for x64

* installing *source* package 'MACPET' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Stage_0_FastqFilteringSubFunctions.cpp -o Stage_0_FastqFilteringSubFunctions.o
Stage_0_FastqFilteringSubFunctions.cpp: In function 'SEXPREC* FilterFastqYield_fun_Rcpp(int&, std::vector<std::__cxx11::basic_string<char> >&, Rcpp::NumericVector&, std::vector<std::__cxx11::basic_string<char> >&, Rcpp::NumericVector&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&)':
Stage_0_FastqFilteringSubFunctions.cpp:55:36: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
         if(SreadFastq1[i].find(NNs)!=-1||SreadFastq2[i].find(NNs)!=-1){
            ~~~~~~~~~~~~~~~~~~~~~~~~^~~~
Stage_0_FastqFilteringSubFunctions.cpp:55:66: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
         if(SreadFastq1[i].find(NNs)!=-1||SreadFastq2[i].find(NNs)!=-1){
                                          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Stage_3_PeakFinderSubFunctions.cpp -o Stage_3_PeakFinderSubFunctions.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:187,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_3_PeakFinderSubFunctions.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h: In function 'Rcpp::List PrepLocFit_Rcpp(Rcpp::DataFrame&, const DataFrame&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h:442:13: warning: 'ChromSize' may be used uninitialized in this function [-Wmaybe-uninitialized]
             r_vector_start<RTYPE>(x)[0] = object;
             ^~~~~~~~~~~~~~
Stage_3_PeakFinderSubFunctions.cpp:61:9: note: 'ChromSize' was declared here
     int ChromSize;//initiate to find them.
         ^~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Stage_4_InteractionsSubFunctions.cpp -o Stage_4_InteractionsSubFunctions.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
Stage_4_InteractionsSubFunctions.cpp: In function 'SEXPREC* Get_NewPeakSummit_fun_Rcpp(const NumericVector&, const NumericVector&, const NumericVector&, const NumericVector&, const int&, const int&)':
Stage_4_InteractionsSubFunctions.cpp:47:39: warning: 'PeakSummit_opt' may be used uninitialized in this function [-Wmaybe-uninitialized]
         PeakSummitNew[MergedPeakCount]=PeakSummit_opt;
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o MACPET.dll tmp.def RcppExports.o Stage_0_FastqFilteringSubFunctions.o Stage_3_PeakFinderSubFunctions.o Stage_4_InteractionsSubFunctions.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/MACPET.buildbin-libdir/MACPET/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MACPET' as MACPET_1.12.0.zip
* DONE (MACPET)