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CHECK report for MACPET on tokay1

This page was generated on 2020-04-15 12:29:55 -0400 (Wed, 15 Apr 2020).

Package 938/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MACPET 1.6.0
Ioannis Vardaxis
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/MACPET
Branch: RELEASE_3_10
Last Commit: 9d500e7
Last Changed Date: 2019-10-29 13:10:59 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MACPET
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MACPET.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings MACPET_1.6.0.tar.gz
StartedAt: 2020-04-15 04:24:22 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 04:31:19 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 417.1 seconds
RetCode: 0
Status:  OK  
CheckDir: MACPET.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MACPET.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings MACPET_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/MACPET.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MACPET/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MACPET' version '1.6.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'MACPET' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/MACPET/libs/i386/MACPET.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/MACPET/libs/x64/MACPET.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
MACPETUlt  5.8   2.29   27.92
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
MACPETUlt  5.3   1.53   28.32
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/MACPET.Rcheck/00check.log'
for details.

Installation output

MACPET.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/MACPET_1.6.0.tar.gz && rm -rf MACPET.buildbin-libdir && mkdir MACPET.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MACPET.buildbin-libdir MACPET_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL MACPET_1.6.0.zip && rm MACPET_1.6.0.tar.gz MACPET_1.6.0.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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  849k  100  849k    0     0  2374k      0 --:--:-- --:--:-- --:--:-- 2392k

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-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/bigmemory/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/bigmemory/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c Stage_0_FastqFilteringSubFunctions.cpp -o Stage_0_FastqFilteringSubFunctions.o
Stage_0_FastqFilteringSubFunctions.cpp: In function 'SEXPREC* FilterFastqYield_fun_Rcpp(int&, std::vector<std::basic_string<char> >&, Rcpp::NumericVector&, std::vector<std::basic_string<char> >&, 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-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/bigmemory/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -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-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/bigmemory/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c Stage_4_InteractionsSubFunctions.cpp -o Stage_4_InteractionsSubFunctions.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/container/map.hpp:30:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:37,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/container/detail/tree.hpp: In instantiation of 'T& boost::container::dtl::tree_node<T, VoidPointer, tree_type_value, OptimizeSize>::get_data() [with T = std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >; VoidPointer = void*; boost::container::tree_type_enum tree_type_value = (boost::container::tree_type_enum)0u; bool OptimizeSize = true]':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/container/detail/iterators.hpp:870:36:   required from 'boost::container::dtl::iterator_from_iiterator<IIterator, IsConst>::reference boost::container::dtl::iterator_from_iiterator<IIterator, IsConst>::operator*() const [with IIterator = boost::intrusive::tree_iterator<boost::intrusive::bhtraits<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits<void*, true>, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, false>; bool IsConst = false; boost::container::dtl::iterator_from_iiterator<IIterator, IsConst>::reference = std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >&]'
C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/container/detail/iterators.hpp:873:87:   required from 'boost::container::dtl::iterator_from_iiterator<IIterator, IsConst>::pointer boost::container::dtl::iterator_from_iiterator<IIterator, IsConst>::operator->() const [with IIterator = boost::intrusive::tree_iterator<boost::intrusive::bhtraits<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits<void*, true>, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, false>; bool IsConst = false; boost::container::dtl::iterator_from_iiterator<IIterator, IsConst>::pointer = std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >*]'
C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:220:41:   required from here
C:/Users/biocbuild/bbs-3.10-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<T*>(this->m_storage.data);   }
                                                        ^
C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/container/detail/tree.hpp: In instantiation of 'const T& boost::container::dtl::tree_node<T, VoidPointer, tree_type_value, OptimizeSize>::get_data() const [with T = std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >; VoidPointer = void*; boost::container::tree_type_enum tree_type_value = (boost::container::tree_type_enum)0u; bool OptimizeSize = true]':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/container/detail/tree.hpp:443:41:   required from 'static const key_type& boost::container::dtl::key_node_compare<KeyCompare, KeyOfValue>::key_from(const boost::container::dtl::tree_node<T, VoidPointer, tree_type_value, OptimizeSize>&) [with T = std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >; 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<const boost::interprocess::ipcdetail::sync_id* const>; boost::container::dtl::key_node_compare<KeyCompare, KeyOfValue>::key_type = const boost::interprocess::ipcdetail::sync_id* const]'
C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/container/detail/tree.hpp:468:60:   required from 'bool boost::container::dtl::key_node_compare<KeyCompare, KeyOfValue>::operator()(const U&, const key_type&) const [with U = boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>; KeyCompare = boost::interprocess::ipcdetail::sync_handles::address_less; KeyOfValue = boost::container::dtl::select1st<const boost::interprocess::ipcdetail::sync_id* const>; boost::container::dtl::key_node_compare<KeyCompare, KeyOfValue>::key_type = const boost::interprocess::ipcdetail::sync_id* const]'
C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/intrusive/detail/tree_value_compare.hpp:175:44:   required from 'Ret boost::intrusive::tree_value_compare<ValuePtr, KeyCompare, KeyOfValue, Ret, true>::operator()(const key_type&, const U&, typename boost::intrusive::disable_if_smartref_to<U, ValuePtr>::type*) const [with U = const boost::interprocess::ipcdetail::sync_id*; ValuePtr = boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>*; KeyCompare = boost::container::dtl::key_node_compare<boost::interprocess::ipcdetail::sync_handles::address_less, boost::container::dtl::select1st<const boost::interprocess::ipcdetail::sync_id* const> >; KeyOfValue = boost::move_detail::identity<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true> >; Ret = bool; boost::intrusive::tree_value_compare<ValuePtr, KeyCompare, KeyOfValue, Ret, true>::key_type = boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>; typename boost::intrusive::disable_if_smartref_to<U, ValuePtr>::type = boost::move_detail::enable_if_nat]'
C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/intrusive/detail/key_nodeptr_comp.hpp:104:19:   required from 'bool boost::intrusive::detail::key_nodeptr_comp<KeyTypeKeyCompare, ValueTraits, KeyOfValue>::operator()(const T1&, const T2&, typename boost::move_detail::enable_if_c<(boost::intrusive::detail::key_nodeptr_comp<KeyTypeKeyCompare, ValueTraits, KeyOfValue>::is_same_or_nodeptr_convertible<T1>::value && (! boost::intrusive::detail::key_nodeptr_comp<KeyTypeKeyCompare, ValueTraits, KeyOfValue>::is_same_or_nodeptr_convertible<T2>::value)), boost::intrusive::detail::key_nodeptr_comp<KeyTypeKeyCompare, ValueTraits, KeyOfValue>::sfinae_type*>::type) const [with T1 = boost::intrusive::compact_rbtree_node<void*>*; T2 = const boost::interprocess::ipcdetail::sync_id*; KeyTypeKeyCompare = boost::container::dtl::key_node_compare<boost::interprocess::ipcdetail::sync_handles::address_less, boost::container::dtl::select1st<const boost::interprocess::ipcdetail::sync_id* const> >; ValueTraits = boost::intrusive::bhtraits<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits<void*, true>, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>; KeyOfValue = boost::move_detail::identity<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true> >; typename boost::move_detail::enable_if_c<(boost::intrusive::detail::key_nodeptr_comp<KeyTypeKeyCompare, ValueTraits, KeyOfValue>::is_same_or_nodeptr_convertible<T1>::value && (! boost::intrusive::detail::key_nodeptr_comp<KeyTypeKeyCompare, ValueTraits, KeyOfValue>::is_same_or_nodeptr_convertible<T2>::value)), boost::intrusive::detail::key_nodeptr_comp<KeyTypeKeyCompare, ValueTraits, KeyOfValue>::sfinae_type*>::type = boost::intrusive::detail::key_nodeptr_comp<boost::container::dtl::key_node_compare<boost::interprocess::ipcdetail::sync_handles::address_less, boost::container::dtl::select1st<const boost::interprocess::ipcdetail::sync_id* const> >, boost::intrusive::bhtraits<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits<void*, true>, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, boost::move_detail::identity<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true> > >::sfinae_type*]'
C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/intrusive/bstree_algorithms.hpp:2028:24:   required from 'static boost::intrusive::bstree_algorithms<NodeTraits>::node_ptr boost::intrusive::bstree_algorithms<NodeTraits>::lower_bound_loop(boost::intrusive::bstree_algorithms<NodeTraits>::node_ptr, boost::intrusive::bstree_algorithms<NodeTraits>::node_ptr, const KeyType&, KeyNodePtrCompare) [with KeyType = const boost::interprocess::ipcdetail::sync_id*; KeyNodePtrCompare = boost::intrusive::detail::key_nodeptr_comp<boost::container::dtl::key_node_compare<boost::interprocess::ipcdetail::sync_handles::address_less, boost::container::dtl::select1st<const boost::interprocess::ipcdetail::sync_id* const> >, boost::intrusive::bhtraits<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits<void*, true>, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, boost::move_detail::identity<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true> > >; NodeTraits = boost::intrusive::rbtree_node_traits<void*, true>; boost::intrusive::bstree_algorithms<NodeTraits>::node_ptr = boost::intrusive::compact_rbtree_node<void*>*]'
C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/intrusive/bstree_algorithms.hpp:920:96:   required from 'static boost::intrusive::bstree_algorithms<NodeTraits>::node_ptr boost::intrusive::bstree_algorithms<NodeTraits>::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::container::dtl::key_node_compare<boost::interprocess::ipcdetail::sync_handles::address_less, boost::container::dtl::select1st<const boost::interprocess::ipcdetail::sync_id* const> >, boost::intrusive::bhtraits<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits<void*, true>, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, boost::move_detail::identity<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true> > >; NodeTraits = boost::intrusive::rbtree_node_traits<void*, true>; boost::intrusive::bstree_algorithms<NodeTraits>::node_ptr = boost::intrusive::compact_rbtree_node<void*>*; boost::intrusive::bstree_algorithms<NodeTraits>::const_node_ptr = const boost::intrusive::compact_rbtree_node<void*>*]'
C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/intrusive/bstree.hpp:334:61:   required from 'boost::intrusive::bstbase2<ValueTraits, VoidOrKeyOfValue, VoidOrKeyComp, AlgoType, HeaderHolder>::iterator boost::intrusive::bstbase2<ValueTraits, VoidOrKeyOfValue, VoidOrKeyComp, AlgoType, HeaderHolder>::lower_bound(const KeyType&, KeyTypeKeyCompare) [with KeyType = const boost::interprocess::ipcdetail::sync_id*; KeyTypeKeyCompare = boost::container::dtl::key_node_compare<boost::interprocess::ipcdetail::sync_handles::address_less, boost::container::dtl::select1st<const boost::interprocess::ipcdetail::sync_id* const> >; ValueTraits = boost::intrusive::bhtraits<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits<void*, true>, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>; VoidOrKeyOfValue = void; VoidOrKeyComp = boost::container::value_to_node_compare<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::tree_value_compare<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >*, boost::interprocess::ipcdetail::sync_handles::address_less, boost::container::dtl::select1st<const boost::interprocess::ipcdetail::sync_id* const>, bool, false>, bool>; boost::intrusive::algo_types AlgoType = (boost::intrusive::algo_types)5u; HeaderHolder = void; boost::intrusive::bstbase2<ValueTraits, VoidOrKeyOfValue, VoidOrKeyComp, AlgoType, HeaderHolder>::iterator = boost::intrusive::tree_iterator<boost::intrusive::bhtraits<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits<void*, true>, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, false>]'
C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/container/detail/tree.hpp:1370:79:   required from 'boost::container::dtl::tree<T, KeyOfValue, Compare, Allocator, Options>::iterator boost::container::dtl::tree<T, KeyOfValue, Compare, Allocator, Options>::lower_bound(const key_type&) [with T = std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >; KeyOfValue = int; Compare = boost::interprocess::ipcdetail::sync_handles::address_less; Allocator = void; Options = void; boost::container::dtl::tree<T, KeyOfValue, Compare, Allocator, Options>::iterator = boost::container::dtl::iterator_from_iiterator<boost::intrusive::tree_iterator<boost::intrusive::bhtraits<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits<void*, true>, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, false>, false>; typename boost::container::dtl::intrusive_tree_type<typename boost::container::real_allocator<T, Allocator>::type, boost::intrusive::tree_value_compare<typename boost::container::allocator_traits<typename boost::container::real_allocator<T, Allocator>::type>::pointer, Compare, typename boost::container::dtl::real_key_of_value<T, KeyOfValue>::type>, typename boost::container::dtl::get_tree_opt<Options>::type:: tree_type, typename boost::container::dtl::get_tree_opt<Options>::type:: optimize_size>::type::iterator = boost::intrusive::tree_iterator<boost::intrusive::bhtraits<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits<void*, true>, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, false>; boost::container::dtl::tree<T, KeyOfValue, Compare, Allocator, Options>::key_type = const boost::interprocess::ipcdetail::sync_id* const]'
C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:217:56:   required from here
C:/Users/biocbuild/bbs-3.10-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<const T*>(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-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-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-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/bigmemory/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/bigmemory/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c Stage_0_FastqFilteringSubFunctions.cpp -o Stage_0_FastqFilteringSubFunctions.o
Stage_0_FastqFilteringSubFunctions.cpp: In function 'SEXPREC* FilterFastqYield_fun_Rcpp(int&, std::vector<std::basic_string<char> >&, Rcpp::NumericVector&, std::vector<std::basic_string<char> >&, 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-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/bigmemory/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -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-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/bigmemory/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c Stage_4_InteractionsSubFunctions.cpp -o Stage_4_InteractionsSubFunctions.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/container/map.hpp:30:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:37,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/interprocess/mapped_region.hpp:50,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:9,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/container/detail/tree.hpp: In instantiation of 'T& boost::container::dtl::tree_node<T, VoidPointer, tree_type_value, OptimizeSize>::get_data() [with T = std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >; VoidPointer = void*; boost::container::tree_type_enum tree_type_value = (boost::container::tree_type_enum)0u; bool OptimizeSize = true]':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/container/detail/iterators.hpp:870:36:   required from 'boost::container::dtl::iterator_from_iiterator<IIterator, IsConst>::reference boost::container::dtl::iterator_from_iiterator<IIterator, IsConst>::operator*() const [with IIterator = boost::intrusive::tree_iterator<boost::intrusive::bhtraits<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits<void*, true>, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, false>; bool IsConst = false; boost::container::dtl::iterator_from_iiterator<IIterator, IsConst>::reference = std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >&]'
C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/container/detail/iterators.hpp:873:87:   required from 'boost::container::dtl::iterator_from_iiterator<IIterator, IsConst>::pointer boost::container::dtl::iterator_from_iiterator<IIterator, IsConst>::operator->() const [with IIterator = boost::intrusive::tree_iterator<boost::intrusive::bhtraits<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits<void*, true>, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, false>; bool IsConst = false; boost::container::dtl::iterator_from_iiterator<IIterator, IsConst>::pointer = std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >*]'
C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:220:41:   required from here
C:/Users/biocbuild/bbs-3.10-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<T*>(this->m_storage.data);   }
                                                        ^
C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/container/detail/tree.hpp: In instantiation of 'const T& boost::container::dtl::tree_node<T, VoidPointer, tree_type_value, OptimizeSize>::get_data() const [with T = std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >; VoidPointer = void*; boost::container::tree_type_enum tree_type_value = (boost::container::tree_type_enum)0u; bool OptimizeSize = true]':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/container/detail/tree.hpp:443:41:   required from 'static const key_type& boost::container::dtl::key_node_compare<KeyCompare, KeyOfValue>::key_from(const boost::container::dtl::tree_node<T, VoidPointer, tree_type_value, OptimizeSize>&) [with T = std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >; 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<const boost::interprocess::ipcdetail::sync_id* const>; boost::container::dtl::key_node_compare<KeyCompare, KeyOfValue>::key_type = const boost::interprocess::ipcdetail::sync_id* const]'
C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/container/detail/tree.hpp:468:60:   required from 'bool boost::container::dtl::key_node_compare<KeyCompare, KeyOfValue>::operator()(const U&, const key_type&) const [with U = boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>; KeyCompare = boost::interprocess::ipcdetail::sync_handles::address_less; KeyOfValue = boost::container::dtl::select1st<const boost::interprocess::ipcdetail::sync_id* const>; boost::container::dtl::key_node_compare<KeyCompare, KeyOfValue>::key_type = const boost::interprocess::ipcdetail::sync_id* const]'
C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/intrusive/detail/tree_value_compare.hpp:175:44:   required from 'Ret boost::intrusive::tree_value_compare<ValuePtr, KeyCompare, KeyOfValue, Ret, true>::operator()(const key_type&, const U&, typename boost::intrusive::disable_if_smartref_to<U, ValuePtr>::type*) const [with U = const boost::interprocess::ipcdetail::sync_id*; ValuePtr = boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>*; KeyCompare = boost::container::dtl::key_node_compare<boost::interprocess::ipcdetail::sync_handles::address_less, boost::container::dtl::select1st<const boost::interprocess::ipcdetail::sync_id* const> >; KeyOfValue = boost::move_detail::identity<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true> >; Ret = bool; boost::intrusive::tree_value_compare<ValuePtr, KeyCompare, KeyOfValue, Ret, true>::key_type = boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>; typename boost::intrusive::disable_if_smartref_to<U, ValuePtr>::type = boost::move_detail::enable_if_nat]'
C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/intrusive/detail/key_nodeptr_comp.hpp:104:19:   required from 'bool boost::intrusive::detail::key_nodeptr_comp<KeyTypeKeyCompare, ValueTraits, KeyOfValue>::operator()(const T1&, const T2&, typename boost::move_detail::enable_if_c<(boost::intrusive::detail::key_nodeptr_comp<KeyTypeKeyCompare, ValueTraits, KeyOfValue>::is_same_or_nodeptr_convertible<T1>::value && (! boost::intrusive::detail::key_nodeptr_comp<KeyTypeKeyCompare, ValueTraits, KeyOfValue>::is_same_or_nodeptr_convertible<T2>::value)), boost::intrusive::detail::key_nodeptr_comp<KeyTypeKeyCompare, ValueTraits, KeyOfValue>::sfinae_type*>::type) const [with T1 = boost::intrusive::compact_rbtree_node<void*>*; T2 = const boost::interprocess::ipcdetail::sync_id*; KeyTypeKeyCompare = boost::container::dtl::key_node_compare<boost::interprocess::ipcdetail::sync_handles::address_less, boost::container::dtl::select1st<const boost::interprocess::ipcdetail::sync_id* const> >; ValueTraits = boost::intrusive::bhtraits<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits<void*, true>, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>; KeyOfValue = boost::move_detail::identity<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true> >; typename boost::move_detail::enable_if_c<(boost::intrusive::detail::key_nodeptr_comp<KeyTypeKeyCompare, ValueTraits, KeyOfValue>::is_same_or_nodeptr_convertible<T1>::value && (! boost::intrusive::detail::key_nodeptr_comp<KeyTypeKeyCompare, ValueTraits, KeyOfValue>::is_same_or_nodeptr_convertible<T2>::value)), boost::intrusive::detail::key_nodeptr_comp<KeyTypeKeyCompare, ValueTraits, KeyOfValue>::sfinae_type*>::type = boost::intrusive::detail::key_nodeptr_comp<boost::container::dtl::key_node_compare<boost::interprocess::ipcdetail::sync_handles::address_less, boost::container::dtl::select1st<const boost::interprocess::ipcdetail::sync_id* const> >, boost::intrusive::bhtraits<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits<void*, true>, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, boost::move_detail::identity<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true> > >::sfinae_type*]'
C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/intrusive/bstree_algorithms.hpp:2028:24:   required from 'static boost::intrusive::bstree_algorithms<NodeTraits>::node_ptr boost::intrusive::bstree_algorithms<NodeTraits>::lower_bound_loop(boost::intrusive::bstree_algorithms<NodeTraits>::node_ptr, boost::intrusive::bstree_algorithms<NodeTraits>::node_ptr, const KeyType&, KeyNodePtrCompare) [with KeyType = const boost::interprocess::ipcdetail::sync_id*; KeyNodePtrCompare = boost::intrusive::detail::key_nodeptr_comp<boost::container::dtl::key_node_compare<boost::interprocess::ipcdetail::sync_handles::address_less, boost::container::dtl::select1st<const boost::interprocess::ipcdetail::sync_id* const> >, boost::intrusive::bhtraits<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits<void*, true>, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, boost::move_detail::identity<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true> > >; NodeTraits = boost::intrusive::rbtree_node_traits<void*, true>; boost::intrusive::bstree_algorithms<NodeTraits>::node_ptr = boost::intrusive::compact_rbtree_node<void*>*]'
C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/intrusive/bstree_algorithms.hpp:920:96:   required from 'static boost::intrusive::bstree_algorithms<NodeTraits>::node_ptr boost::intrusive::bstree_algorithms<NodeTraits>::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::container::dtl::key_node_compare<boost::interprocess::ipcdetail::sync_handles::address_less, boost::container::dtl::select1st<const boost::interprocess::ipcdetail::sync_id* const> >, boost::intrusive::bhtraits<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits<void*, true>, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, boost::move_detail::identity<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true> > >; NodeTraits = boost::intrusive::rbtree_node_traits<void*, true>; boost::intrusive::bstree_algorithms<NodeTraits>::node_ptr = boost::intrusive::compact_rbtree_node<void*>*; boost::intrusive::bstree_algorithms<NodeTraits>::const_node_ptr = const boost::intrusive::compact_rbtree_node<void*>*]'
C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/intrusive/bstree.hpp:334:61:   required from 'boost::intrusive::bstbase2<ValueTraits, VoidOrKeyOfValue, VoidOrKeyComp, AlgoType, HeaderHolder>::iterator boost::intrusive::bstbase2<ValueTraits, VoidOrKeyOfValue, VoidOrKeyComp, AlgoType, HeaderHolder>::lower_bound(const KeyType&, KeyTypeKeyCompare) [with KeyType = const boost::interprocess::ipcdetail::sync_id*; KeyTypeKeyCompare = boost::container::dtl::key_node_compare<boost::interprocess::ipcdetail::sync_handles::address_less, boost::container::dtl::select1st<const boost::interprocess::ipcdetail::sync_id* const> >; ValueTraits = boost::intrusive::bhtraits<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits<void*, true>, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>; VoidOrKeyOfValue = void; VoidOrKeyComp = boost::container::value_to_node_compare<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::tree_value_compare<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >*, boost::interprocess::ipcdetail::sync_handles::address_less, boost::container::dtl::select1st<const boost::interprocess::ipcdetail::sync_id* const>, bool, false>, bool>; boost::intrusive::algo_types AlgoType = (boost::intrusive::algo_types)5u; HeaderHolder = void; boost::intrusive::bstbase2<ValueTraits, VoidOrKeyOfValue, VoidOrKeyComp, AlgoType, HeaderHolder>::iterator = boost::intrusive::tree_iterator<boost::intrusive::bhtraits<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits<void*, true>, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, false>]'
C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/container/detail/tree.hpp:1370:79:   required from 'boost::container::dtl::tree<T, KeyOfValue, Compare, Allocator, Options>::iterator boost::container::dtl::tree<T, KeyOfValue, Compare, Allocator, Options>::lower_bound(const key_type&) [with T = std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >; KeyOfValue = int; Compare = boost::interprocess::ipcdetail::sync_handles::address_less; Allocator = void; Options = void; boost::container::dtl::tree<T, KeyOfValue, Compare, Allocator, Options>::iterator = boost::container::dtl::iterator_from_iiterator<boost::intrusive::tree_iterator<boost::intrusive::bhtraits<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits<void*, true>, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, false>, false>; typename boost::container::dtl::intrusive_tree_type<typename boost::container::real_allocator<T, Allocator>::type, boost::intrusive::tree_value_compare<typename boost::container::allocator_traits<typename boost::container::real_allocator<T, Allocator>::type>::pointer, Compare, typename boost::container::dtl::real_key_of_value<T, KeyOfValue>::type>, typename boost::container::dtl::get_tree_opt<Options>::type:: tree_type, typename boost::container::dtl::get_tree_opt<Options>::type:: optimize_size>::type::iterator = boost::intrusive::tree_iterator<boost::intrusive::bhtraits<boost::container::dtl::tree_node<std::pair<const boost::interprocess::ipcdetail::sync_id* const, boost::unordered::iterator_detail::iterator<boost::unordered::detail::ptr_node<std::pair<const boost::interprocess::ipcdetail::sync_id, void*> > > >, void*, (boost::container::tree_type_enum)0u, true>, boost::intrusive::rbtree_node_traits<void*, true>, (boost::intrusive::link_mode_type)0u, boost::intrusive::dft_tag, 3u>, false>; boost::container::dtl::tree<T, KeyOfValue, Compare, Allocator, Options>::key_type = const boost::interprocess::ipcdetail::sync_id* const]'
C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/interprocess/sync/windows/sync_utils.hpp:217:56:   required from here
C:/Users/biocbuild/bbs-3.10-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<const T*>(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-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/MACPET.buildbin-libdir/MACPET/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MACPET' as MACPET_1.6.0.zip
* DONE (MACPET)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'MACPET' successfully unpacked and MD5 sums checked

Tests output

Example timings

MACPET.Rcheck/examples_i386/MACPET-Ex.timings

nameusersystemelapsed
AnalysisStatistics0.110.021.14
ConvertToPE_BAM2.230.392.80
ConvertToPSelf0.340.000.35
GetShortestPath0.070.001.54
GetSignInteractions0.120.000.13
MACPETUlt 5.80 2.2927.92
PeaksToGRanges0.060.000.06
PeaksToNarrowPeak0.140.000.14
TagsToGInteractions0.080.000.08
exportPeaks000
plot3.450.073.52
summary0.520.000.51

MACPET.Rcheck/examples_x64/MACPET-Ex.timings

nameusersystemelapsed
AnalysisStatistics0.060.000.07
ConvertToPE_BAM3.110.253.72
ConvertToPSelf0.270.010.28
GetShortestPath0.070.020.11
GetSignInteractions0.110.000.11
MACPETUlt 5.30 1.5328.32
PeaksToGRanges0.060.000.07
PeaksToNarrowPeak0.140.000.14
TagsToGInteractions0.070.000.06
exportPeaks0.000.020.01
plot3.450.003.46
summary0.590.030.62