Mike Jiang
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/CytoML |
| git_branch: RELEASE_3_13 |
| git_last_commit: 6e64d69 |
| git_last_commit_date: 2021-05-19 12:21:29 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:02 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the CytoML package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CytoML.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 435/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CytoML 2.4.0 (landing page) Mike Jiang
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: CytoML |
| Version: 2.4.0 |
| Command: rm -rf CytoML.buildbin-libdir && mkdir CytoML.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CytoML.buildbin-libdir CytoML_2.4.0.tar.gz |
| StartedAt: 2021-10-15 08:50:32 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 08:54:50 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 257.8 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: CytoML_2.4.0.zip |
| PackageFileSize: 14.47 MiB |
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###
### Running command:
###
### rm -rf CytoML.buildbin-libdir && mkdir CytoML.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CytoML.buildbin-libdir CytoML_2.4.0.tar.gz
###
##############################################################################
##############################################################################
install for i386
* installing *source* package 'CytoML' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
rm -f RcppExports.o parseFlowJoWorkspace.o CytoML.dll
"C:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386/Rscript.exe" "../tools/winlibs.R" 2.9.8
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include/ -I../windows/libxml2-2.9.8/include/libxml2 -DLIBXML_STATIC -fpermissive -DRCPP_PARALLEL_USE_TBB=1 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
In file included from ../inst/include/CytoML/openWorkspace.hpp:12,
from ../inst/include/CytoML.h:5,
from RcppExports.cpp:4:
../inst/include/CytoML/winFlowJoWorkspace.hpp:435:30: warning: "/*" within comment [-Wcomment]
* "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
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_<Pred>::************
^
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-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-3.13-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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
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::__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-3.13-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-3.13-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)
~~^~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
^~~~~~~~
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
^~~~~~~~
In file included from C:/rtools40/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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
^~~~~~~~
In file included from C:/rtools40/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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
^~~~~~~~
In file included from C:/rtools40/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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
^~~~~~~~
In file included from C:/rtools40/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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr<Y> & r )
^~~~~~~~
In file included from C:/rtools40/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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr<Y> && r )
^~~~~~~~
In file included from C:/rtools40/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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
^~~~~~~~
In file included from C:/rtools40/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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
BOOST_HEADER_DEPRECATED("<iterator>")
^
In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from ../inst/include/CytoML.h:5,
from RcppExports.cpp:4:
../inst/include/CytoML/flowJoWorkspace.hpp: In member function 'std::vector<CytoML::SampleInfo> CytoML::flowJoWorkspace::get_sample_info(const std::vector<int, std::allocator<int> >&, const CytoML::ParseWorkspaceParameters&)':
../inst/include/CytoML/flowJoWorkspace.hpp:598:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
for(int j = 0; j < sample_ids.size(); j++)
~~^~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include/ -I../windows/libxml2-2.9.8/include/libxml2 -DLIBXML_STATIC -fpermissive -DRCPP_PARALLEL_USE_TBB=1 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c parseFlowJoWorkspace.cpp -o parseFlowJoWorkspace.o
In file included from ../inst/include/CytoML/openWorkspace.hpp:12,
from parseFlowJoWorkspace.cpp:9:
../inst/include/CytoML/winFlowJoWorkspace.hpp:435:30: warning: "/*" within comment [-Wcomment]
* "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
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_<Pred>::************
^
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
C:/Users/biocbuild/bbs-3.13-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-3.13-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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
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::__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-3.13-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-3.13-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)
~~^~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/CytoML/workspace.hpp:14,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
^~~~~~~~
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/CytoML/workspace.hpp:14,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
^~~~~~~~
In file included from C:/rtools40/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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/CytoML/workspace.hpp:14,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
^~~~~~~~
In file included from C:/rtools40/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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/CytoML/workspace.hpp:14,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
^~~~~~~~
In file included from C:/rtools40/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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/CytoML/workspace.hpp:14,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
^~~~~~~~
In file included from C:/rtools40/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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/CytoML/workspace.hpp:14,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr<Y> & r )
^~~~~~~~
In file included from C:/rtools40/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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/CytoML/workspace.hpp:14,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr<Y> && r )
^~~~~~~~
In file included from C:/rtools40/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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/CytoML/workspace.hpp:14,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
^~~~~~~~
In file included from C:/rtools40/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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/CytoML/workspace.hpp:14,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
BOOST_HEADER_DEPRECATED("<iterator>")
^
In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
../inst/include/CytoML/flowJoWorkspace.hpp: In member function 'std::vector<CytoML::SampleInfo> CytoML::flowJoWorkspace::get_sample_info(const std::vector<int, std::allocator<int> >&, const CytoML::ParseWorkspaceParameters&)':
../inst/include/CytoML/flowJoWorkspace.hpp:598:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
for(int j = 0; j < sample_ids.size(); j++)
~~^~~~~~~~~~~~~~~~~~~
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o CytoML.dll tmp.def RcppExports.o parseFlowJoWorkspace.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -L../windows/libxml2-2.9.8/lib/i386 -lxml2 -llzma -liconv -lz 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/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/lib/i386 -ltbb -ltbbmalloc -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 -lws2_32 -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/CytoML.buildbin-libdir/00LOCK-CytoML/00new/CytoML/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CytoML'
finding HTML links ... done
CytoML-deprecated html
CytoML.par.get html
CytoML.par.init html
addCustomInfo html
ce_get_channels html
ce_get_compensations html
ce_get_markers html
ce_get_panels html
ce_get_samples html
ce_get_transformations html
compensate-GatingSet-graphGML-method html
constructTree html
cytobank_experiment-methods html
cytobank_to_gatingset html
diva_get_samples html
diva_to_gatingset html
diva_workspace-class html
finding level-2 HTML links ... done
extend html
fj_ws_get_keywords html
fj_ws_get_sample_groups html
fj_ws_get_samples html
flowjo_to_gatingset html
flowjo_workspace-class html
gatingset_to_cytobank html
gatingset_to_flowjo html
getChildren-graphGML-character-method html
getCompensationMatrices.graphGML html
getGate-graphGML-character-method html
getNodes-graphGML-method html
getParent-graphGML-character-method html
getTransformations.graphGML html
graphGML-class html
gs_compare_cytobank_counts html
matchPath html
open_cytobank_experiment html
open_diva_xml html
open_flowjo_xml html
parse.gateInfo html
plot-graphGML-missing-method html
range.GatingHierarchy html
read.gatingML.cytobank html
show-graphGML-method html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'CytoML' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
rm -f RcppExports.o parseFlowJoWorkspace.o CytoML.dll
"C:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64/Rscript.exe" "../tools/winlibs.R" 2.9.8
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include/ -I../windows/libxml2-2.9.8/include/libxml2 -DLIBXML_STATIC -fpermissive -DRCPP_PARALLEL_USE_TBB=1 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
In file included from ../inst/include/CytoML/openWorkspace.hpp:12,
from ../inst/include/CytoML.h:5,
from RcppExports.cpp:4:
../inst/include/CytoML/winFlowJoWorkspace.hpp:435:30: warning: "/*" within comment [-Wcomment]
* "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
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_<Pred>::************
^
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-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-3.13-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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
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::__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-3.13-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-3.13-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)
~~^~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
^~~~~~~~
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr<Y> & r )
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr<Y> && r )
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from ../inst/include/CytoML.h:4,
from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
BOOST_HEADER_DEPRECATED("<iterator>")
^
In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from ../inst/include/CytoML.h:5,
from RcppExports.cpp:4:
../inst/include/CytoML/flowJoWorkspace.hpp: In member function 'std::vector<CytoML::SampleInfo> CytoML::flowJoWorkspace::get_sample_info(const std::vector<int, std::allocator<int> >&, const CytoML::ParseWorkspaceParameters&)':
../inst/include/CytoML/flowJoWorkspace.hpp:598:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int j = 0; j < sample_ids.size(); j++)
~~^~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include/ -I../windows/libxml2-2.9.8/include/libxml2 -DLIBXML_STATIC -fpermissive -DRCPP_PARALLEL_USE_TBB=1 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c parseFlowJoWorkspace.cpp -o parseFlowJoWorkspace.o
In file included from ../inst/include/CytoML/openWorkspace.hpp:12,
from parseFlowJoWorkspace.cpp:9:
../inst/include/CytoML/winFlowJoWorkspace.hpp:435:30: warning: "/*" within comment [-Wcomment]
* "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
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_<Pred>::************
^
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
C:/Users/biocbuild/bbs-3.13-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-3.13-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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
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::__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-3.13-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-3.13-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)
~~^~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/CytoML/workspace.hpp:14,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
^~~~~~~~
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/CytoML/workspace.hpp:14,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/CytoML/workspace.hpp:14,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/CytoML/workspace.hpp:14,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/CytoML/workspace.hpp:14,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/CytoML/workspace.hpp:14,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr<Y> & r )
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/CytoML/workspace.hpp:14,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr<Y> && r )
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/CytoML/workspace.hpp:14,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/CytoML/workspace.hpp:14,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
BOOST_HEADER_DEPRECATED("<iterator>")
^
In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:9:
../inst/include/CytoML/flowJoWorkspace.hpp: In member function 'std::vector<CytoML::SampleInfo> CytoML::flowJoWorkspace::get_sample_info(const std::vector<int, std::allocator<int> >&, const CytoML::ParseWorkspaceParameters&)':
../inst/include/CytoML/flowJoWorkspace.hpp:598:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int j = 0; j < sample_ids.size(); j++)
~~^~~~~~~~~~~~~~~~~~~
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o CytoML.dll tmp.def RcppExports.o parseFlowJoWorkspace.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -L../windows/libxml2-2.9.8/lib/x64 -lxml2 -llzma -liconv -lz 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/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -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 -lws2_32 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/CytoML.buildbin-libdir/CytoML/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CytoML' as CytoML_2.4.0.zip
* DONE (CytoML)