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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/MACPET_1.8.0.tar.gz && rm -rf MACPET.buildbin-libdir && mkdir MACPET.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MACPET.buildbin-libdir MACPET_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL MACPET_1.8.0.zip && rm MACPET_1.8.0.tar.gz MACPET_1.8.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 851k 100 851k 0 0 7012k 0 --:--:-- --:--:-- --:--:-- 7341k
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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:178,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_3_PeakFinderSubFunctions.cpp:1:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h: In function 'Rcpp::List PrepLocFit_Rcpp(Rcpp::DataFrame&, const DataFrame&)':
C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: 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-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: 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-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: 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-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: 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-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: 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-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: 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-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: 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-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include' -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:178,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_3_PeakFinderSubFunctions.cpp:1:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h: In function 'Rcpp::List PrepLocFit_Rcpp(Rcpp::DataFrame&, const DataFrame&)':
C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: 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-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: 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-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: 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-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: 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-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: 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-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: 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-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/date_time/microsec_time_clock.hpp:18,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/detail/posix_time_types_wrk.hpp:31,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/sync/spin/mutex.hpp:24,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:25,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: 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-3.11-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/MACPET.buildbin-libdir/MACPET/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MACPET' as MACPET_1.8.0.zip
* DONE (MACPET)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'MACPET' successfully unpacked and MD5 sums checked
