############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL MACPET ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘MACPET’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -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 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 unsigned int’} and ‘int’ [-Wsign-compare] 55 | if(SreadFastq1[i].find(NNs)!=-1||SreadFastq2[i].find(NNs)!=-1){ | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c Stage_3_PeakFinderSubFunctions.cpp -o Stage_3_PeakFinderSubFunctions.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c Stage_4_InteractionsSubFunctions.cpp -o Stage_4_InteractionsSubFunctions.o In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10, from /home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4, from Stage_4_InteractionsSubFunctions.cpp:4: /home/biocbuild/bbs-3.13-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 /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27, from Stage_4_InteractionsSubFunctions.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10, from /home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4, from Stage_4_InteractionsSubFunctions.cpp:4: /home/biocbuild/bbs-3.13-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 /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27, from Stage_4_InteractionsSubFunctions.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10, from /home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4, from Stage_4_InteractionsSubFunctions.cpp:4: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 465 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27, from Stage_4_InteractionsSubFunctions.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10, from /home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4, from Stage_4_InteractionsSubFunctions.cpp:4: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 478 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27, from Stage_4_InteractionsSubFunctions.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10, from /home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4, from Stage_4_InteractionsSubFunctions.cpp:4: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 561 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27, from Stage_4_InteractionsSubFunctions.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10, from /home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4, from Stage_4_InteractionsSubFunctions.cpp:4: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 570 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27, from Stage_4_InteractionsSubFunctions.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10, from /home/biocbuild/bbs-3.13-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4, from Stage_4_InteractionsSubFunctions.cpp:4: /home/biocbuild/bbs-3.13-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>&&)’: /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 572 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:27, from Stage_4_InteractionsSubFunctions.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | 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++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o MACPET.so RcppExports.o Stage_0_FastqFilteringSubFunctions.o Stage_3_PeakFinderSubFunctions.o Stage_4_InteractionsSubFunctions.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-MACPET/00new/MACPET/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MACPET)