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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/flowCore_2.6.0.tar.gz && rm -rf flowCore.buildbin-libdir && mkdir flowCore.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowCore.buildbin-libdir flowCore_2.6.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL flowCore_2.6.0.zip && rm flowCore_2.6.0.tar.gz flowCore_2.6.0.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
8 8848k 8 752k 0 0 874k 0 0:00:10 --:--:-- 0:00:10 875k
28 8848k 28 2525k 0 0 1356k 0 0:00:06 0:00:01 0:00:05 1357k
59 8848k 59 5221k 0 0 1823k 0 0:00:04 0:00:02 0:00:02 1823k
99 8848k 99 8818k 0 0 2281k 0 0:00:03 0:00:03 --:--:-- 2282k
100 8848k 100 8848k 0 0 2289k 0 0:00:03 0:00:03 --:--:-- 2289k
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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from C:/Users/biocbuild/bbs-3.14-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-3.14-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-3.14-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_<Pred>::************
^
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function.hpp:30,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from C:/Users/biocbuild/bbs-3.14-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-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
template<class T> T * get_pointer(std::auto_ptr<T> const& p)
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
from C:/Users/biocbuild/bbs-3.14-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<typename> class auto_ptr;
^~~~~~~~
In file included from pairVectorRcppWrap.h:10,
from flowCore_types.h:12,
from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from fcsTextParse.cpp:8:
C:/Users/biocbuild/bbs-3.14-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-3.14-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_<Pred>::************
^
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function.hpp:30,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
from fcsTextParse.cpp:8:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
template<class T> T * get_pointer(std::auto_ptr<T> 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-3.14-bioc/R/library/BH/include/boost/algorithm/string/classification.hpp:15,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:23,
from C:/Users/biocbuild/bbs-3.14-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<typename> class auto_ptr;
^~~~~~~~
In file included from pairVectorRcppWrap.h:10,
from fcsTextParse.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from pairVectorRcppWrap.h:10,
from pairVectorRcppWrap.cpp:7:
C:/Users/biocbuild/bbs-3.14-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-3.14-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_<Pred>::************
^
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function.hpp:30,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from pairVectorRcppWrap.h:10,
from pairVectorRcppWrap.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
template<class T> T * get_pointer(std::auto_ptr<T> const& p)
^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
from C:/Users/biocbuild/bbs-3.14-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<typename> class auto_ptr;
^~~~~~~~
In file included from pairVectorRcppWrap.h:10,
from pairVectorRcppWrap.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3.14-bioc/R/library/cytolib/lib/i386/libcytolib.a C:/Users/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/lib/i386/GatingSet.pb.o -LC:/Users/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/lib/i386 -lprotobuf -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/library/Rhdf5lib/lib/i386 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRblas -lstdc++fs -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/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-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from C:/Users/biocbuild/bbs-3.14-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-3.14-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-3.14-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_<Pred>::************
^
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function.hpp:30,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from C:/Users/biocbuild/bbs-3.14-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-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
template<class T> T * get_pointer(std::auto_ptr<T> const& p)
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
from C:/Users/biocbuild/bbs-3.14-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<typename> class auto_ptr;
^~~~~~~~
In file included from pairVectorRcppWrap.h:10,
from flowCore_types.h:12,
from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from fcsTextParse.cpp:8:
C:/Users/biocbuild/bbs-3.14-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-3.14-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_<Pred>::************
^
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function.hpp:30,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
from fcsTextParse.cpp:8:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
template<class T> T * get_pointer(std::auto_ptr<T> 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-3.14-bioc/R/library/BH/include/boost/algorithm/string/classification.hpp:15,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:23,
from C:/Users/biocbuild/bbs-3.14-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<typename> class auto_ptr;
^~~~~~~~
In file included from pairVectorRcppWrap.h:10,
from fcsTextParse.cpp:10:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from pairVectorRcppWrap.h:10,
from pairVectorRcppWrap.cpp:7:
C:/Users/biocbuild/bbs-3.14-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-3.14-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_<Pred>::************
^
In file included from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function.hpp:30,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from pairVectorRcppWrap.h:10,
from pairVectorRcppWrap.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
template<class T> T * get_pointer(std::auto_ptr<T> const& p)
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
from C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
from C:/Users/biocbuild/bbs-3.14-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<typename> class auto_ptr;
^~~~~~~~
In file included from pairVectorRcppWrap.h:10,
from pairVectorRcppWrap.cpp:7:
C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.14-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-3.14-bioc/R/library/cytolib/lib/x64/libcytolib.a C:/Users/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/lib/x64/GatingSet.pb.o -LC:/Users/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/lib/x64 -lprotobuf -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRblas -lstdc++fs -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/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-3.14-bioc/meat/flowCore.buildbin-libdir/flowCore/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowCore' as flowCore_2.6.0.zip
* DONE (flowCore)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'flowCore' successfully unpacked and MD5 sums checked
