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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/MACPET_1.4.0.tar.gz && rm -rf MACPET.buildbin-libdir && mkdir MACPET.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MACPET.buildbin-libdir MACPET_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL MACPET_1.4.0.zip && rm MACPET_1.4.0.tar.gz MACPET_1.4.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 852k 100 852k 0 0 11.8M 0 --:--:-- --:--:-- --:--:-- 13.2M
install for i386
* installing *source* package 'MACPET' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/bigmemory/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/bigmemory/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -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 between signed and unsigned integer expressions [-Wsign-compare]
if(SreadFastq1[i].find(NNs)!=-1||SreadFastq2[i].find(NNs)!=-1){
^
Stage_0_FastqFilteringSubFunctions.cpp:55:66: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(SreadFastq1[i].find(NNs)!=-1||SreadFastq2[i].find(NNs)!=-1){
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/bigmemory/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Stage_3_PeakFinderSubFunctions.cpp -o Stage_3_PeakFinderSubFunctions.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/bigmemory/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Stage_4_InteractionsSubFunctions.cpp -o Stage_4_InteractionsSubFunctions.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/container/map.hpp:30:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:37,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/container/detail/tree.hpp: In instantiation of 'T& boost::container::dtl::tree_node::get_data() [with T = std::pair > > >; VoidPointer = void*; boost::container::tree_type_enum tree_type_value = (boost::container::tree_type_enum)0u; bool OptimizeSize = true]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/container/detail/iterators.hpp:854:36: required from 'boost::container::dtl::iterator_from_iiterator::reference boost::container::dtl::iterator_from_iiterator::operator*() const [with IIterator = boost::intrusive::tree_iterator > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, false>; bool IsConst = false; boost::container::dtl::iterator_from_iiterator::reference = std::pair > > >&]'
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/container/detail/iterators.hpp:857:87: required from 'boost::container::dtl::iterator_from_iiterator::pointer boost::container::dtl::iterator_from_iiterator::operator->() const [with IIterator = boost::intrusive::tree_iterator > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, false>; bool IsConst = false; boost::container::dtl::iterator_from_iiterator::pointer = std::pair > > >*]'
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:220:41: required from here
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/container/detail/tree.hpp:148:56: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
{ return *reinterpret_cast(this->m_storage.data); }
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/container/detail/tree.hpp: In instantiation of 'const T& boost::container::dtl::tree_node::get_data() const [with T = std::pair > > >; VoidPointer = void*; boost::container::tree_type_enum tree_type_value = (boost::container::tree_type_enum)0u; bool OptimizeSize = true]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/container/detail/tree.hpp:443:41: required from 'static const key_type& boost::container::dtl::key_node_compare::key_from(const boost::container::dtl::tree_node&) [with T = std::pair > > >; VoidPointer = void*; boost::container::tree_type_enum tree_type_value = (boost::container::tree_type_enum)0u; bool OptimizeSize = true; KeyCompare = boost::interprocess::ipcdetail::sync_handles::address_less; KeyOfValue = boost::container::dtl::select1st; boost::container::dtl::key_node_compare::key_type = const boost::interprocess::ipcdetail::sync_id*]'
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/container/detail/tree.hpp:468:60: required from 'bool boost::container::dtl::key_node_compare::operator()(const U&, const key_type&) const [with U = boost::container::dtl::tree_node > > >, void*, (boost::container::tree_type_enum)0u, true>; KeyCompare = boost::interprocess::ipcdetail::sync_handles::address_less; KeyOfValue = boost::container::dtl::select1st; boost::container::dtl::key_node_compare::key_type = const boost::interprocess::ipcdetail::sync_id*]'
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/intrusive/detail/tree_value_compare.hpp:175:44: required from 'Ret boost::intrusive::tree_value_compare::operator()(const key_type&, const U&, typename boost::intrusive::disable_if_smartref_to::type*) const [with U = const boost::interprocess::ipcdetail::sync_id*; ValuePtr = boost::container::dtl::tree_node > > >, void*, (boost::container::tree_type_enum)0u, true>*; KeyCompare = boost::container::dtl::key_node_compare >; KeyOfValue = boost::move_detail::identity > > >, void*, (boost::container::tree_type_enum)0u, true> >; Ret = bool; boost::intrusive::tree_value_compare::key_type = boost::container::dtl::tree_node > > >, void*, (boost::container::tree_type_enum)0u, true>; typename boost::intrusive::disable_if_smartref_to::type = void]'
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/intrusive/detail/key_nodeptr_comp.hpp:104:19: required from 'bool boost::intrusive::detail::key_nodeptr_comp::operator()(const T1&, const T2&, typename boost::move_detail::enable_if_c<(boost::intrusive::detail::key_nodeptr_comp::is_same_or_nodeptr_convertible::value && (! boost::intrusive::detail::key_nodeptr_comp::is_same_or_nodeptr_convertible::value)), boost::intrusive::detail::key_nodeptr_comp::sfinae_type*>::type) const [with T1 = boost::intrusive::compact_rbtree_node*; T2 = const boost::interprocess::ipcdetail::sync_id*; KeyTypeKeyCompare = boost::container::dtl::key_node_compare >; ValueTraits = boost::intrusive::bhtraits > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>; KeyOfValue = boost::move_detail::identity > > >, void*, (boost::container::tree_type_enum)0u, true> >; typename boost::move_detail::enable_if_c<(boost::intrusive::detail::key_nodeptr_comp::is_same_or_nodeptr_convertible::value && (! boost::intrusive::detail::key_nodeptr_comp::is_same_or_nodeptr_convertible::value)), boost::intrusive::detail::key_nodeptr_comp::sfinae_type*>::type = boost::intrusive::detail::key_nodeptr_comp >, boost::intrusive::bhtraits > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, boost::move_detail::identity > > >, void*, (boost::container::tree_type_enum)0u, true> > >::sfinae_type*]'
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/intrusive/bstree_algorithms.hpp:2028:24: required from 'static boost::intrusive::bstree_algorithms::node_ptr boost::intrusive::bstree_algorithms::lower_bound_loop(boost::intrusive::bstree_algorithms::node_ptr, boost::intrusive::bstree_algorithms::node_ptr, const KeyType&, KeyNodePtrCompare) [with KeyType = const boost::interprocess::ipcdetail::sync_id*; KeyNodePtrCompare = boost::intrusive::detail::key_nodeptr_comp >, boost::intrusive::bhtraits > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, boost::move_detail::identity > > >, void*, (boost::container::tree_type_enum)0u, true> > >; NodeTraits = boost::intrusive::rbtree_node_traits; boost::intrusive::bstree_algorithms::node_ptr = boost::intrusive::compact_rbtree_node*]'
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/intrusive/bstree_algorithms.hpp:920:96: required from 'static boost::intrusive::bstree_algorithms::node_ptr boost::intrusive::bstree_algorithms::lower_bound(const const_node_ptr&, const KeyType&, KeyNodePtrCompare) [with KeyType = const boost::interprocess::ipcdetail::sync_id*; KeyNodePtrCompare = boost::intrusive::detail::key_nodeptr_comp >, boost::intrusive::bhtraits > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, boost::move_detail::identity > > >, void*, (boost::container::tree_type_enum)0u, true> > >; NodeTraits = boost::intrusive::rbtree_node_traits; boost::intrusive::bstree_algorithms::node_ptr = boost::intrusive::compact_rbtree_node*; boost::intrusive::bstree_algorithms::const_node_ptr = const boost::intrusive::compact_rbtree_node*]'
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/intrusive/bstree.hpp:334:61: required from 'boost::intrusive::bstbase2::iterator boost::intrusive::bstbase2::lower_bound(const KeyType&, KeyTypeKeyCompare) [with KeyType = const boost::interprocess::ipcdetail::sync_id*; KeyTypeKeyCompare = boost::container::dtl::key_node_compare >; ValueTraits = boost::intrusive::bhtraits > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>; VoidOrKeyOfValue = void; VoidOrKeyComp = boost::container::value_to_node_compare > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::tree_value_compare > > >*, boost::interprocess::ipcdetail::sync_handles::address_less, boost::container::dtl::select1st, bool, false>, bool>; boost::intrusive::algo_types AlgoType = (boost::intrusive::algo_types)5u; HeaderHolder = void; boost::intrusive::bstbase2::iterator = boost::intrusive::tree_iterator > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, false>]'
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/container/detail/tree.hpp:1337:79: required from 'boost::container::dtl::tree::iterator boost::container::dtl::tree::lower_bound(const key_type&) [with T = std::pair > > >; KeyOfValue = boost::container::dtl::select1st; Compare = boost::interprocess::ipcdetail::sync_handles::address_less; Allocator = boost::container::new_allocator > > > >; Options = void; boost::container::dtl::tree::iterator = boost::container::dtl::iterator_from_iiterator > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, false>, false>; typename boost::container::dtl::intrusive_tree_type::pointer, Compare, KeyOfValue>, typename boost::container::dtl::get_tree_opt::type:: tree_type, typename boost::container::dtl::get_tree_opt::type:: optimize_size>::type::iterator = boost::intrusive::tree_iterator > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, false>; boost::container::dtl::tree::key_type = const boost::interprocess::ipcdetail::sync_id*]'
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:217:56: required from here
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/container/detail/tree.hpp:151:62: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
{ return *reinterpret_cast(this->m_storage.data); }
^
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:47:54: warning: 'PeakSummit_opt' may be used uninitialized in this function [-Wmaybe-uninitialized]
PeakSummitNew[MergedPeakCount]=PeakSummit_opt;
^
C:/Rtools/mingw_32/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-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-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:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/bigmemory/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/bigmemory/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -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 between signed and unsigned integer expressions [-Wsign-compare]
if(SreadFastq1[i].find(NNs)!=-1||SreadFastq2[i].find(NNs)!=-1){
^
Stage_0_FastqFilteringSubFunctions.cpp:55:66: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(SreadFastq1[i].find(NNs)!=-1||SreadFastq2[i].find(NNs)!=-1){
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/bigmemory/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Stage_3_PeakFinderSubFunctions.cpp -o Stage_3_PeakFinderSubFunctions.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/bigmemory/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Stage_4_InteractionsSubFunctions.cpp -o Stage_4_InteractionsSubFunctions.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/container/map.hpp:30:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:37,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/container/detail/tree.hpp: In instantiation of 'T& boost::container::dtl::tree_node::get_data() [with T = std::pair > > >; VoidPointer = void*; boost::container::tree_type_enum tree_type_value = (boost::container::tree_type_enum)0u; bool OptimizeSize = true]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/container/detail/iterators.hpp:854:36: required from 'boost::container::dtl::iterator_from_iiterator::reference boost::container::dtl::iterator_from_iiterator::operator*() const [with IIterator = boost::intrusive::tree_iterator > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, false>; bool IsConst = false; boost::container::dtl::iterator_from_iiterator::reference = std::pair > > >&]'
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/container/detail/iterators.hpp:857:87: required from 'boost::container::dtl::iterator_from_iiterator::pointer boost::container::dtl::iterator_from_iiterator::operator->() const [with IIterator = boost::intrusive::tree_iterator > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, false>; bool IsConst = false; boost::container::dtl::iterator_from_iiterator::pointer = std::pair > > >*]'
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:220:41: required from here
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/container/detail/tree.hpp:148:56: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
{ return *reinterpret_cast(this->m_storage.data); }
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/container/detail/tree.hpp: In instantiation of 'const T& boost::container::dtl::tree_node::get_data() const [with T = std::pair > > >; VoidPointer = void*; boost::container::tree_type_enum tree_type_value = (boost::container::tree_type_enum)0u; bool OptimizeSize = true]':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/container/detail/tree.hpp:443:41: required from 'static const key_type& boost::container::dtl::key_node_compare::key_from(const boost::container::dtl::tree_node&) [with T = std::pair > > >; VoidPointer = void*; boost::container::tree_type_enum tree_type_value = (boost::container::tree_type_enum)0u; bool OptimizeSize = true; KeyCompare = boost::interprocess::ipcdetail::sync_handles::address_less; KeyOfValue = boost::container::dtl::select1st; boost::container::dtl::key_node_compare::key_type = const boost::interprocess::ipcdetail::sync_id*]'
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/container/detail/tree.hpp:468:60: required from 'bool boost::container::dtl::key_node_compare::operator()(const U&, const key_type&) const [with U = boost::container::dtl::tree_node > > >, void*, (boost::container::tree_type_enum)0u, true>; KeyCompare = boost::interprocess::ipcdetail::sync_handles::address_less; KeyOfValue = boost::container::dtl::select1st; boost::container::dtl::key_node_compare::key_type = const boost::interprocess::ipcdetail::sync_id*]'
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/intrusive/detail/tree_value_compare.hpp:175:44: required from 'Ret boost::intrusive::tree_value_compare::operator()(const key_type&, const U&, typename boost::intrusive::disable_if_smartref_to::type*) const [with U = const boost::interprocess::ipcdetail::sync_id*; ValuePtr = boost::container::dtl::tree_node > > >, void*, (boost::container::tree_type_enum)0u, true>*; KeyCompare = boost::container::dtl::key_node_compare >; KeyOfValue = boost::move_detail::identity > > >, void*, (boost::container::tree_type_enum)0u, true> >; Ret = bool; boost::intrusive::tree_value_compare::key_type = boost::container::dtl::tree_node > > >, void*, (boost::container::tree_type_enum)0u, true>; typename boost::intrusive::disable_if_smartref_to::type = void]'
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/intrusive/detail/key_nodeptr_comp.hpp:104:19: required from 'bool boost::intrusive::detail::key_nodeptr_comp::operator()(const T1&, const T2&, typename boost::move_detail::enable_if_c<(boost::intrusive::detail::key_nodeptr_comp::is_same_or_nodeptr_convertible::value && (! boost::intrusive::detail::key_nodeptr_comp::is_same_or_nodeptr_convertible::value)), boost::intrusive::detail::key_nodeptr_comp::sfinae_type*>::type) const [with T1 = boost::intrusive::compact_rbtree_node*; T2 = const boost::interprocess::ipcdetail::sync_id*; KeyTypeKeyCompare = boost::container::dtl::key_node_compare >; ValueTraits = boost::intrusive::bhtraits > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>; KeyOfValue = boost::move_detail::identity > > >, void*, (boost::container::tree_type_enum)0u, true> >; typename boost::move_detail::enable_if_c<(boost::intrusive::detail::key_nodeptr_comp::is_same_or_nodeptr_convertible::value && (! boost::intrusive::detail::key_nodeptr_comp::is_same_or_nodeptr_convertible::value)), boost::intrusive::detail::key_nodeptr_comp::sfinae_type*>::type = boost::intrusive::detail::key_nodeptr_comp >, boost::intrusive::bhtraits > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, boost::move_detail::identity > > >, void*, (boost::container::tree_type_enum)0u, true> > >::sfinae_type*]'
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/intrusive/bstree_algorithms.hpp:2028:24: required from 'static boost::intrusive::bstree_algorithms::node_ptr boost::intrusive::bstree_algorithms::lower_bound_loop(boost::intrusive::bstree_algorithms::node_ptr, boost::intrusive::bstree_algorithms::node_ptr, const KeyType&, KeyNodePtrCompare) [with KeyType = const boost::interprocess::ipcdetail::sync_id*; KeyNodePtrCompare = boost::intrusive::detail::key_nodeptr_comp >, boost::intrusive::bhtraits > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, boost::move_detail::identity > > >, void*, (boost::container::tree_type_enum)0u, true> > >; NodeTraits = boost::intrusive::rbtree_node_traits; boost::intrusive::bstree_algorithms::node_ptr = boost::intrusive::compact_rbtree_node*]'
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/intrusive/bstree_algorithms.hpp:920:96: required from 'static boost::intrusive::bstree_algorithms::node_ptr boost::intrusive::bstree_algorithms::lower_bound(const const_node_ptr&, const KeyType&, KeyNodePtrCompare) [with KeyType = const boost::interprocess::ipcdetail::sync_id*; KeyNodePtrCompare = boost::intrusive::detail::key_nodeptr_comp >, boost::intrusive::bhtraits > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, boost::move_detail::identity > > >, void*, (boost::container::tree_type_enum)0u, true> > >; NodeTraits = boost::intrusive::rbtree_node_traits; boost::intrusive::bstree_algorithms::node_ptr = boost::intrusive::compact_rbtree_node*; boost::intrusive::bstree_algorithms::const_node_ptr = const boost::intrusive::compact_rbtree_node*]'
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/intrusive/bstree.hpp:334:61: required from 'boost::intrusive::bstbase2::iterator boost::intrusive::bstbase2::lower_bound(const KeyType&, KeyTypeKeyCompare) [with KeyType = const boost::interprocess::ipcdetail::sync_id*; KeyTypeKeyCompare = boost::container::dtl::key_node_compare >; ValueTraits = boost::intrusive::bhtraits > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>; VoidOrKeyOfValue = void; VoidOrKeyComp = boost::container::value_to_node_compare > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::tree_value_compare > > >*, boost::interprocess::ipcdetail::sync_handles::address_less, boost::container::dtl::select1st, bool, false>, bool>; boost::intrusive::algo_types AlgoType = (boost::intrusive::algo_types)5u; HeaderHolder = void; boost::intrusive::bstbase2::iterator = boost::intrusive::tree_iterator > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, false>]'
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/container/detail/tree.hpp:1337:79: required from 'boost::container::dtl::tree::iterator boost::container::dtl::tree::lower_bound(const key_type&) [with T = std::pair > > >; KeyOfValue = boost::container::dtl::select1st; Compare = boost::interprocess::ipcdetail::sync_handles::address_less; Allocator = boost::container::new_allocator > > > >; Options = void; boost::container::dtl::tree::iterator = boost::container::dtl::iterator_from_iiterator > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, false>, false>; typename boost::container::dtl::intrusive_tree_type::pointer, Compare, KeyOfValue>, typename boost::container::dtl::get_tree_opt::type:: tree_type, typename boost::container::dtl::get_tree_opt::type:: optimize_size>::type::iterator = boost::intrusive::tree_iterator > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, false>; boost::container::dtl::tree::key_type = const boost::interprocess::ipcdetail::sync_id*]'
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:217:56: required from here
C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/container/detail/tree.hpp:151:62: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
{ return *reinterpret_cast(this->m_storage.data); }
^
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:47:54: warning: 'PeakSummit_opt' may be used uninitialized in this function [-Wmaybe-uninitialized]
PeakSummitNew[MergedPeakCount]=PeakSummit_opt;
^
C:/Rtools/mingw_64/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-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/MACPET.buildbin-libdir/MACPET/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MACPET' as MACPET_1.4.0.zip
* DONE (MACPET)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'MACPET' successfully unpacked and MD5 sums checked
