############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL CytoML ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’ * installing *source* package ‘CytoML’ ... ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ -std=gnu++11 accepts -g... yes checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed configure: setting xml2 flags... configure: No directory was specified for --with-xml2. Trying to find xml2 using other methods. checking for xml2-config... /usr/bin/xml2-config configure: setting cytolib-ml commandline tool path... configure: Using the following compilation and linking flags configure: PKG_CPPFLAGS=-I/usr/include/libxml2 configure: PKG_LIBS=-lxml2 -lz -llzma -lm configure: CYTOLIBML_BIN=/usr/local/bin configure: creating ./config.status config.status: creating src/Makevars config.status: creating R/cytolibml_bin_path.R ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cpp11/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/flowWorkspace/include' -I/usr/local/include -fPIC -g -O2 -Wall -c cpp11.cpp -o cpp11.o In file included from ../inst/include/CytoML/openWorkspace.hpp:12, from CytoML_types.h:5, from cpp11.cpp:4: ../inst/include/CytoML/winFlowJoWorkspace.hpp:435:30: warning: "/*" within comment [-Wcomment] 435 | * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate | In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/range/iterator_range.hpp:13, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/range/as_literal.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/algorithm/string/trim.hpp:19, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/algorithm/string.hpp:19, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/transformation.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/compensation.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/CytoFrame.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/gate.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/POPINDICES.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/nodeProperties.hpp:13, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/populationTree.hpp:13, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/GatingSet.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/flowWorkspace/include/flowWorkspace.h:5, from CytoML_types.h:4, from cpp11.cpp:4: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/CytoFrame.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/gate.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/POPINDICES.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/nodeProperties.hpp:13, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/populationTree.hpp:13, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/GatingSet.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/flowWorkspace/include/flowWorkspace.h:5, from CytoML_types.h:4, from cpp11.cpp:4: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 58 | if(valVec.size() != 1+n+n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 62 | if(valVec.size() == 1+n+2*n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) | ~~^~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/flowWorkspace/include/flowWorkspace.h:6, from CytoML_types.h:4, from cpp11.cpp:4: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/flowWorkspace/include/flowWorkspace/pairVectorCpp11Convert.h: In function ‘cpp11::writable::doubles_matrix<> arma_to_rmatrix(const mat&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/flowWorkspace/include/flowWorkspace/pairVectorCpp11Convert.h:33:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 33 | for (auto j = 0; j < m; j++) { | ~~^~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/flowWorkspace/include/flowWorkspace/pairVectorCpp11Convert.h:34:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 34 | for (auto i = 0; i < n; i++) { | ~~^~~ In file included 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 CytoML_types.h:5, from cpp11.cpp:4: ../inst/include/CytoML/wsNode.hpp: In member function ‘virtual std::streamsize CytoML::Cytostreambuf::xsputn(const char*, std::streamsize)’: ../inst/include/CytoML/wsNode.hpp:27:20: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 2 has type ‘std::streamsize’ {aka ‘long int’} [-Wformat=] 27 | Rprintf("%.*s", n, s); | ~~^~ ~ | | | | int std::streamsize {aka long int} In file included 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 CytoML_types.h:5, from cpp11.cpp:4: ../inst/include/CytoML/workspace_type.hpp: In function ‘std::vector, std::allocator > > CytoML::list_files(const string&, const string&)’: ../inst/include/CytoML/workspace_type.hpp:67:124: warning: ‘boost::filesystem::recursive_directory_iterator::recursive_directory_iterator(const boost::filesystem::path&, boost::filesystem::symlink_option)’ is deprecated: Use directory_options instead of symlink_option [-Wdeprecated-declarations] 67 | for(const fs::directory_entry & i: fs::recursive_directory_iterator(fs::path(data_dir), fs::symlink_option::recurse)) | ^ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/filesystem.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/CytoVFS.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/global.hpp:21, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/compensation.hpp:19, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/CytoFrame.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/gate.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/POPINDICES.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/nodeProperties.hpp:13, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/populationTree.hpp:13, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/GatingSet.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/flowWorkspace/include/flowWorkspace.h:5, from CytoML_types.h:4, from cpp11.cpp:4: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/filesystem/directory.hpp:923:5: note: declared here 923 | recursive_directory_iterator(path const& dir_path, BOOST_SCOPED_ENUM_NATIVE(symlink_option) opts) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10, from ../inst/include/CytoML/openWorkspace.hpp:11, from CytoML_types.h:5, from cpp11.cpp:4: ../inst/include/CytoML/flowJoWorkspace.hpp: In member function ‘std::unique_ptr CytoML::flowJoWorkspace::to_GatingSet(unsigned int, CytoML::ParseWorkspaceParameters, cytolib::GatingSet&)’: ../inst/include/CytoML/flowJoWorkspace.hpp:201:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 201 | for (int i = 0; i < sample_infos.size(); i++) | ~~^~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10, from ../inst/include/CytoML/openWorkspace.hpp:11, from CytoML_types.h:5, from cpp11.cpp:4: ../inst/include/CytoML/flowJoWorkspace.hpp: In member function ‘std::vector CytoML::flowJoWorkspace::get_sample_info(const std::vector >&, const CytoML::ParseWorkspaceParameters&)’: ../inst/include/CytoML/flowJoWorkspace.hpp:585:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 585 | for(int j = 0; j < sample_ids.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cpp11/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/flowWorkspace/include' -I/usr/local/include -fPIC -g -O2 -Wall -c parseFlowJoWorkspace.cpp -o parseFlowJoWorkspace.o In file included from ../inst/include/CytoML/openWorkspace.hpp:12, from parseFlowJoWorkspace.cpp:10: ../inst/include/CytoML/winFlowJoWorkspace.hpp:435:30: warning: "/*" within comment [-Wcomment] 435 | * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate | In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/range/iterator_range.hpp:13, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/range/as_literal.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/algorithm/string/trim.hpp:19, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/algorithm/string.hpp:19, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/transformation.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/compensation.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/CytoFrame.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/gate.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/POPINDICES.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-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:10: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/CytoFrame.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/gate.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/POPINDICES.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-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:10: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 58 | if(valVec.size() != 1+n+n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 62 | if(valVec.size() == 1+n+2*n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2) | ~~^~~~~~~~~~~~~~~~~~~~~ In file included 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:10: ../inst/include/CytoML/wsNode.hpp: In member function ‘virtual std::streamsize CytoML::Cytostreambuf::xsputn(const char*, std::streamsize)’: ../inst/include/CytoML/wsNode.hpp:27:20: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 2 has type ‘std::streamsize’ {aka ‘long int’} [-Wformat=] 27 | Rprintf("%.*s", n, s); | ~~^~ ~ | | | | int std::streamsize {aka long int} In file included 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:10: ../inst/include/CytoML/workspace_type.hpp: In function ‘std::vector, std::allocator > > CytoML::list_files(const string&, const string&)’: ../inst/include/CytoML/workspace_type.hpp:67:124: warning: ‘boost::filesystem::recursive_directory_iterator::recursive_directory_iterator(const boost::filesystem::path&, boost::filesystem::symlink_option)’ is deprecated: Use directory_options instead of symlink_option [-Wdeprecated-declarations] 67 | for(const fs::directory_entry & i: fs::recursive_directory_iterator(fs::path(data_dir), fs::symlink_option::recurse)) | ^ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/filesystem.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/CytoVFS.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/global.hpp:21, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/compensation.hpp:19, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/CytoFrame.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/gate.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/include/cytolib/POPINDICES.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-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:10: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/filesystem/directory.hpp:923:5: note: declared here 923 | recursive_directory_iterator(path const& dir_path, BOOST_SCOPED_ENUM_NATIVE(symlink_option) opts) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10, from ../inst/include/CytoML/openWorkspace.hpp:11, from parseFlowJoWorkspace.cpp:10: ../inst/include/CytoML/flowJoWorkspace.hpp: In member function ‘std::unique_ptr CytoML::flowJoWorkspace::to_GatingSet(unsigned int, CytoML::ParseWorkspaceParameters, cytolib::GatingSet&)’: ../inst/include/CytoML/flowJoWorkspace.hpp:201:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 201 | for (int i = 0; i < sample_infos.size(); i++) | ~~^~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10, from ../inst/include/CytoML/openWorkspace.hpp:11, from parseFlowJoWorkspace.cpp:10: ../inst/include/CytoML/flowJoWorkspace.hpp: In member function ‘std::vector CytoML::flowJoWorkspace::get_sample_info(const std::vector >&, const CytoML::ParseWorkspaceParameters&)’: ../inst/include/CytoML/flowJoWorkspace.hpp:585:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 585 | for(int j = 0; j < sample_ids.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/flowWorkspace/include/flowWorkspace.h:6, from parseFlowJoWorkspace.cpp:11: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/flowWorkspace/include/flowWorkspace/pairVectorCpp11Convert.h: In function ‘cpp11::writable::doubles_matrix<> arma_to_rmatrix(const mat&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/flowWorkspace/include/flowWorkspace/pairVectorCpp11Convert.h:33:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 33 | for (auto j = 0; j < m; j++) { | ~~^~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/flowWorkspace/include/flowWorkspace/pairVectorCpp11Convert.h:34:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 34 | for (auto i = 0; i < n; i++) { | ~~^~~ parseFlowJoWorkspace.cpp: In function ‘cpp11::external_pointer parse_workspace(cpp11::external_pointer, int, cpp11::list, bool, std::string, cpp11::external_pointer, std::string, std::string, bool, std::vector, std::allocator > >, bool, std::vector, std::allocator > >, bool, bool, float, float, bool, bool, bool, bool, cpp11::list, bool, std::string, bool, SEXP, int)’: parseFlowJoWorkspace.cpp:103:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 103 | for(int i = 0; i < filter_names.size(); i++) | ~~^~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o CytoML.so cpp11.o parseFlowJoWorkspace.o /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/cytolib/lib/libcytolib.a /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -lopenblas -lxml2 -lz -llzma -lm -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-CytoML/00new/CytoML/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (CytoML)