############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * 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 >&, Rcpp::NumericVector&, std::vector >&, 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::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::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(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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( 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 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 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & 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 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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && 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 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& boost::shared_ptr::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 std::auto_ptr' is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( 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 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)