##############################################################################
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###
### Running command:
###
### rm -rf MACPET.buildbin-libdir && mkdir MACPET.buildbin-libdir && F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=MACPET.buildbin-libdir MACPET_1.15.1.tar.gz
###
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* installing *source* package 'MACPET' ...
** using staged installation
** libs
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fexceptions -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fexceptions -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::string&, std::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]
55 | 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]
55 | if(SreadFastq1[i].find(NNs)!=-1||SreadFastq2[i].find(NNs)!=-1){
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fexceptions -c Stage_3_PeakFinderSubFunctions.cpp -o Stage_3_PeakFinderSubFunctions.o
In file included from F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/RcppCommon.h:187,
from F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_3_PeakFinderSubFunctions.cpp:1:
F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h: In function 'Rcpp::List PrepLocFit_Rcpp(Rcpp::DataFrame&, const DataFrame&)':
F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h:442:41: warning: 'ChromSize' may be used uninitialized in this function [-Wmaybe-uninitialized]
442 | r_vector_start<RTYPE>(x)[0] = object;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
Stage_3_PeakFinderSubFunctions.cpp:61:9: note: 'ChromSize' was declared here
61 | int ChromSize;//initiate to find them.
| ^~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fexceptions -c Stage_4_InteractionsSubFunctions.cpp -o Stage_4_InteractionsSubFunctions.o
In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from F:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
from F:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
F:/biocbuild/bbs-3.15-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]
361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\locale_conv.h:41,
from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\locale:43,
from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\iomanip:43,
from F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_4_InteractionsSubFunctions.cpp:1:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from F:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
from F:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\locale_conv.h:41,
from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\locale:43,
from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\iomanip:43,
from F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_4_InteractionsSubFunctions.cpp:1:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from F:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
from F:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
507 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\locale_conv.h:41,
from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\locale:43,
from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\iomanip:43,
from F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_4_InteractionsSubFunctions.cpp:1:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from F:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
from F:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
520 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\locale_conv.h:41,
from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\locale:43,
from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\iomanip:43,
from F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_4_InteractionsSubFunctions.cpp:1:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from F:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
from F:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
603 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\locale_conv.h:41,
from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\locale:43,
from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\iomanip:43,
from F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_4_InteractionsSubFunctions.cpp:1:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from F:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
from F:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
612 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\locale_conv.h:41,
from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\locale:43,
from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\iomanip:43,
from F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_4_InteractionsSubFunctions.cpp:1:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from F:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
from F:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
F:/biocbuild/bbs-3.15-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>&&)':
F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
614 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\locale_conv.h:41,
from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\locale:43,
from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\iomanip:43,
from F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp.h:27,
from Stage_4_InteractionsSubFunctions.cpp:1:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | 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]
47 | PeakSummitNew[MergedPeakCount]=PeakSummit_opt;
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:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.15-bioc/meat/MACPET.buildbin-libdir/00LOCK-MACPET/00new/MACPET/libs/x64
** 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
* MD5 sums
packaged installation of 'MACPET' as MACPET_1.15.1.zip
* DONE (MACPET)
