############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/flowCore_2.4.0.tar.gz && rm -rf flowCore.buildbin-libdir && mkdir flowCore.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowCore.buildbin-libdir flowCore_2.4.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL flowCore_2.4.0.zip && rm flowCore_2.4.0.tar.gz flowCore_2.4.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 43 8843k 43 3860k 0 0 5351k 0 0:00:01 --:--:-- 0:00:01 5353k 100 8843k 100 8843k 0 0 7045k 0 0:00:01 0:00:01 --:--:-- 7052k install for i386 * installing *source* package 'flowCore' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FastLogicle.cpp -o FastLogicle.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Hyperlog.cpp -o Hyperlog.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Logicle.cpp -o Logicle.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from pairVectorRcppWrap.h:10, from flowCore_types.h:12, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function.hpp:30, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from pairVectorRcppWrap.h:10, from flowCore_types.h:12, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from pairVectorRcppWrap.h:10, from flowCore_types.h:12, from RcppExports.cpp:4: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from pairVectorRcppWrap.h:10, from flowCore_types.h:12, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector, std::allocator > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector, std::allocator > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, std::allocator > >::size_type' {aka 'unsigned int'} [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c biexponential.cpp -o biexponential.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c convertRawBytes.cpp -o convertRawBytes.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fcsTextParse.cpp -o fcsTextParse.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from fcsTextParse.cpp:8: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function.hpp:30, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:23, from fcsTextParse.cpp:8: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41, from C:/rtools40/mingw32/include/c++/8.3.0/locale:43, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/classification.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from fcsTextParse.cpp:8: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from pairVectorRcppWrap.h:10, from fcsTextParse.cpp:10: C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector, std::allocator > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector, std::allocator > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, std::allocator > >::size_type' {aka 'unsigned int'} [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hyperlogTransform.cpp -o hyperlogTransform.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c inPolygon.cpp -o inPolygon.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c inPolytope.cpp -o inPolytope.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c logicleTransform.cpp -o logicleTransform.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pairVectorRcppWrap.cpp -o pairVectorRcppWrap.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from pairVectorRcppWrap.h:10, from pairVectorRcppWrap.cpp:7: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function.hpp:30, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from pairVectorRcppWrap.h:10, from pairVectorRcppWrap.cpp:7: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from pairVectorRcppWrap.h:10, from pairVectorRcppWrap.cpp:7: C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from pairVectorRcppWrap.h:10, from pairVectorRcppWrap.cpp:7: C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector, std::allocator > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector, std::allocator > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, std::allocator > >::size_type' {aka 'unsigned int'} [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c poly_centroid.cpp -o poly_centroid.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sortBytes.cpp -o sortBytes.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c uint2double.cpp -o uint2double.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zeroin.cpp -o zeroin.o C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o flowCore.dll tmp.def FastLogicle.o Hyperlog.o Logicle.o RcppExports.o biexponential.o convertRawBytes.o fcsTextParse.o hyperlogTransform.o inPolygon.o inPolytope.o logicleTransform.o pairVectorRcppWrap.o poly_centroid.o sortBytes.o uint2double.o zeroin.o C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/lib/i386/libcytolib.a C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/lib/i386/GatingSet.pb.o -LC:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/lib/i386 -lprotobuf -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/library/Rhdf5lib/lib/i386 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRblas -lstdc++fs -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowCore.dll; fi installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/flowCore.buildbin-libdir/00LOCK-flowCore/00new/flowCore/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'flowCore' finding HTML links ... done CytoExploreR_exports html EHtrans-class html FCSTransTransform html GvHD html Subset-methods html arcsinhTransform html asinht-class html asinhtGml2-class html biexponentialTransform html boundaryFilter-class html characterOrNumeric-class html characterOrParameters-class html characterOrTransformation-class html checkOffset html coerce html collapse_desc html compensatedParameter-class html compensation-class html complementFilter-class html concreteFilter-class html decompensate html dg1polynomial-class html each_col html ellipsoidGate-class html estimateMedianLogicle html exponential-class html expressionFilter-class html filter-and-methods html filter-class html filter-in-methods html filter-methods html filter-on-methods html filterDetails-methods html filterList-class html filterReference-class html filterResult-class html filterResultList-class html filterSummary-class html filterSummaryList-class html filters-class html flowCore-package html flowFrame-class html flowSet-class html flowSet_to_list html fr_append_cols html fsApply html getChannelMarker html getIndexSort html hyperlog-class html hyperlogtGml2-class html identifier-methods html intersectFilter-class html inverseLogicleTransform html invsplitscale-class html keyword-methods html kmeansFilter-class html linearTransform html lintGml2-class html lnTransform html logTransform html logarithm-class html logicalFilterResult-class html logicleTransform html logicletGml2-class html logtGml2-class html manyFilterResult-class html markernames html multipleFilterResult-class html normalization-class html nullParameter-class html parameterFilter-class html parameterTransform-class html parameters-class html parameters-methods html polygonGate-class html polytopeGate-class html quadGate-class html quadratic-class html quadraticTransform html randomFilterResult-class html ratio-class html ratiotGml2-class html read.FCS html read.FCSheader html read.flowSet html rectangleGate-class html rotate_gate html sampleFilter-class html scaleTransform html scale_gate html setOperationFilter-class html shift_gate html singleParameterTransform-class html sinht-class html split-methods html splitScaleTransform html splitscale-class html squareroot-class html subsetFilter-class html summarizeFilter-methods html timeFilter-class html transform-class html transform html transformFilter-class html transformList-class html transformMap-class html transformReference-class html transform_gate html transformation-class html truncateTransform html unionFilter-class html unitytransform-class html updateTransformKeywords html validFilters html write.FCS html write.flowSet html ** building package indices ** installing vignettes 'HowTo-flowCore.Rnw' using 'UTF-8' ** 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 'flowCore' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FastLogicle.cpp -o FastLogicle.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Hyperlog.cpp -o Hyperlog.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Logicle.cpp -o Logicle.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from pairVectorRcppWrap.h:10, from flowCore_types.h:12, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function.hpp:30, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from pairVectorRcppWrap.h:10, from flowCore_types.h:12, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from pairVectorRcppWrap.h:10, from flowCore_types.h:12, from RcppExports.cpp:4: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from pairVectorRcppWrap.h:10, from flowCore_types.h:12, from RcppExports.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector, std::allocator > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector, std::allocator > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, std::allocator > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c biexponential.cpp -o biexponential.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c convertRawBytes.cpp -o convertRawBytes.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fcsTextParse.cpp -o fcsTextParse.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from fcsTextParse.cpp:8: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function.hpp:30, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:23, from fcsTextParse.cpp:8: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ 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:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/classification.hpp:15, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from fcsTextParse.cpp:8: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from pairVectorRcppWrap.h:10, from fcsTextParse.cpp:10: C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector, std::allocator > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector, std::allocator > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, std::allocator > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hyperlogTransform.cpp -o hyperlogTransform.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c inPolygon.cpp -o inPolygon.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c inPolytope.cpp -o inPolytope.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c logicleTransform.cpp -o logicleTransform.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pairVectorRcppWrap.cpp -o pairVectorRcppWrap.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from pairVectorRcppWrap.h:10, from pairVectorRcppWrap.cpp:7: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function.hpp:30, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from pairVectorRcppWrap.h:10, from pairVectorRcppWrap.cpp:7: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] template T * get_pointer(std::auto_ptr const& p) ^~~~~~~~ In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from pairVectorRcppWrap.h:10, from pairVectorRcppWrap.cpp:7: C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from pairVectorRcppWrap.h:10, from pairVectorRcppWrap.cpp:7: C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)': C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector, std::allocator > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() != 1+n+n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~ C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector, std::allocator > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] if(valVec.size() == 1+n+2*n*n){ ~~~~~~~~~~~~~~^~~~~~~~~~~~ C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, std::allocator > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) ~~^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c poly_centroid.cpp -o poly_centroid.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sortBytes.cpp -o sortBytes.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c uint2double.cpp -o uint2double.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c zeroin.cpp -o zeroin.o C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o flowCore.dll tmp.def FastLogicle.o Hyperlog.o Logicle.o RcppExports.o biexponential.o convertRawBytes.o fcsTextParse.o hyperlogTransform.o inPolygon.o inPolytope.o logicleTransform.o pairVectorRcppWrap.o poly_centroid.o sortBytes.o uint2double.o zeroin.o C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/lib/x64/libcytolib.a C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/lib/x64/GatingSet.pb.o -LC:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/lib/x64 -lprotobuf -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRblas -lstdc++fs -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowCore.dll; fi installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/flowCore.buildbin-libdir/flowCore/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'flowCore' as flowCore_2.4.0.zip * DONE (flowCore) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'flowCore' successfully unpacked and MD5 sums checked