##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL contiBAIT
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'contiBAIT' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c buildLinkageGroups.cpp -o buildLinkageGroups.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c computeSim.cpp -o computeSim.o
In file included from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:6,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/dynamic_bitset/dynamic_bitset.hpp:53,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/dynamic_bitset.hpp:15,
                 from computeSim.cpp:3:
F:/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/container_hash/hash.hpp:132:33: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  132 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\unordered_map:44,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:62,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:30,
                 from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from computeSim.cpp:2:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/BH/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c orderContigsGreedy.cpp -o orderContigsGreedy.o
g++ -std=gnu++11 -shared -s -static-libgcc -o contiBAIT.dll tmp.def buildLinkageGroups.o computeSim.o orderContigsGreedy.o -lm -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-contiBAIT/00new/contiBAIT/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT'
** testing if installed package keeps a record of temporary installation path
* DONE (contiBAIT)