##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MACPET.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MACPET_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/MACPET.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.15.1'
* 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
* 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 x64 is not available
File 'D:/biocbuild/bbs-3.15-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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
MACPETUlt 4.93   0.64   19.41
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/MACPET.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MACPET
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'MACPET' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Stage_0_FastqFilteringSubFunctions.cpp -o Stage_0_FastqFilteringSubFunctions.o
Stage_0_FastqFilteringSubFunctions.cpp: In function 'SEXPREC* FilterFastqYield_fun_Rcpp(int&, std::vector<std::__cxx11::basic_string<char> >&, Rcpp::NumericVector&, std::vector<std::__cxx11::basic_string<char> >&, Rcpp::NumericVector&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&)':
Stage_0_FastqFilteringSubFunctions.cpp:55:36: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
         if(SreadFastq1[i].find(NNs)!=-1||SreadFastq2[i].find(NNs)!=-1){
            ~~~~~~~~~~~~~~~~~~~~~~~~^~~~
Stage_0_FastqFilteringSubFunctions.cpp:55:66: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
         if(SreadFastq1[i].find(NNs)!=-1||SreadFastq2[i].find(NNs)!=-1){
                                          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Stage_3_PeakFinderSubFunctions.cpp -o Stage_3_PeakFinderSubFunctions.o
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/RcppCommon.h:187,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_3_PeakFinderSubFunctions.cpp:1:
D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h: In function 'Rcpp::List PrepLocFit_Rcpp(Rcpp::DataFrame&, const DataFrame&)':
D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h:442:13: warning: 'ChromSize' may be used uninitialized in this function [-Wmaybe-uninitialized]
             r_vector_start<RTYPE>(x)[0] = object;
             ^~~~~~~~~~~~~~
Stage_3_PeakFinderSubFunctions.cpp:61:9: note: 'ChromSize' was declared here
     int ChromSize;//initiate to find them.
         ^~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c Stage_4_InteractionsSubFunctions.cpp -o Stage_4_InteractionsSubFunctions.o
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_4_InteractionsSubFunctions.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
Stage_4_InteractionsSubFunctions.cpp: In function 'SEXPREC* Get_NewPeakSummit_fun_Rcpp(const NumericVector&, const NumericVector&, const NumericVector&, const NumericVector&, const int&, const int&)':
Stage_4_InteractionsSubFunctions.cpp:47:39: warning: 'PeakSummit_opt' may be used uninitialized in this function [-Wmaybe-uninitialized]
         PeakSummitNew[MergedPeakCount]=PeakSummit_opt;
C:/rtools40/mingw64/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 -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-MACPET/00new/MACPET/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MACPET'
    finding HTML links ... done
    AnalysisStatistics                      html  
    ConvertToPE_BAM                         html  
    ConvertToPSelf                          html  
    GenomeMap-class                         html  
    GetShortestPath                         html  
    GetSignInteractions                     html  
    MACPET                                  html  
    finding level-2 HTML links ... done

    MACPETUlt                               html  
    MACPET_GenomeMapData.rda                html  
    MACPET_pinterData.rda                   html  
    MACPET_pintraData.rda                   html  
    MACPET_pselfData.rda                    html  
    MACPET_psfitData.rda                    html  
    PInter-class                            html  
    PIntra-class                            html  
    PSFit-class                             html  
    PSelf-class                             html  
    PeaksToGRanges                          html  
    PeaksToNarrowPeak                       html  
    SampleChIAPETData.bam                   html  
    SampleChIAPETDataRead_1.bam             html  
    SampleChIAPETDataRead_2.bam             html  
    TagsToGInteractions                     html  
    exportPeaks                             html  
    plot                                    html  
    summary                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MACPET)
Making 'packages.html' ... done