############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL flowWorkspace ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘flowWorkspace’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’ using C++17 g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -w -Wfatal-errors -I'/home/biocbuild/R/R-4.4.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c R_API.cpp -o R_API.o In file included from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:21, from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingSet.hpp:14, from R_API.cpp:9: /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp: In member function 'std::pair cytolib::CytoFrameView::get_range(const std::string&, cytolib::ColType, cytolib::RangeType) const': /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp:260:9: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 260 | { | ^ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -w -Wfatal-errors -I'/home/biocbuild/R/R-4.4.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o In file included from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:21, from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingSet.hpp:14, from R_GatingHierarchy.cpp:18: /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp: In member function 'std::pair cytolib::CytoFrameView::get_range(const std::string&, cytolib::ColType, cytolib::RangeType) const': /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp:260:9: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 260 | { | ^ In file included from /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_algobase.h:64, from /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/specfun.h:43, from /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/cmath:3898, from /home/biocbuild/R/R-4.4.1/site-library/cpp11/include/cpp11/as.hpp:3, from /home/biocbuild/R/R-4.4.1/site-library/cpp11/include/cpp11.hpp:5, from R_GatingHierarchy.cpp:16: /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = float; _T2 = float; typename __strip_reference_wrapper::type>::__type = float; typename decay<_Tp>::type = float; typename __strip_reference_wrapper::type>::__type = float; typename decay<_Tp2>::type = float]': R_GatingHierarchy.cpp:824:22: required from here 824 | std::make_pair(static_cast(ranges_input.at(i)), | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 825 | static_cast(ranges_input.at(i + 1)))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1132 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ In file included from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp:13: /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/H5CytoFrame.hpp: In member function 'virtual void cytolib::H5CytoFrame::set_range(const std::string&, cytolib::ColType, std::pair, bool)': /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/H5CytoFrame.hpp:204:14: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 204 | void set_range(const string & colname, ColType ctype, pair new_range, bool is_update_keywords = true){ | ^~~~~~~~~ R_GatingHierarchy.cpp: In function 'cytolib::gatePtr newGate(cpp11::list)': R_GatingHierarchy.cpp:824:29: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 824 | std::make_pair(static_cast(ranges_input.at(i)), | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 825 | static_cast(ranges_input.at(i + 1)))); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -w -Wfatal-errors -I'/home/biocbuild/R/R-4.4.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c R_GatingSet.cpp -o R_GatingSet.o In file included from flowWorkspace_types.h:7, from R_GatingSet.cpp:10: /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp: In member function 'std::pair cytolib::CytoFrameView::get_range(const std::string&, cytolib::ColType, cytolib::RangeType) const': /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp:260:9: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 260 | { | ^ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -w -Wfatal-errors -I'/home/biocbuild/R/R-4.4.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c cpp11.cpp -o cpp11.o In file included from flowWorkspace_types.h:7, from cpp11.cpp:4: /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp: In member function 'std::pair cytolib::CytoFrameView::get_range(const std::string&, cytolib::ColType, cytolib::RangeType) const': /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp:260:9: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 260 | { | ^ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -w -Wfatal-errors -I'/home/biocbuild/R/R-4.4.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c cytoframeAPI.cpp -o cytoframeAPI.o In file included from cytoframeAPI.cpp:5: /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp: In member function 'std::pair cytolib::CytoFrameView::get_range(const std::string&, cytolib::ColType, cytolib::RangeType) const': /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp:260:9: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 260 | { | ^ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -w -Wfatal-errors -I'/home/biocbuild/R/R-4.4.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c cytosetAPI.cpp -o cytosetAPI.o In file included from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:21, from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingSet.hpp:14, from ../inst/include/flowWorkspace/pairVectorCpp11Convert.h:12, from cytosetAPI.cpp:2: /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp: In member function 'std::pair cytolib::CytoFrameView::get_range(const std::string&, cytolib::ColType, cytolib::RangeType) const': /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp:260:9: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 260 | { | ^ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -w -Wfatal-errors -I'/home/biocbuild/R/R-4.4.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c getDescendants.cpp -o getDescendants.o In file included from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:21, from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingSet.hpp:14, from getDescendants.cpp:1: /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp: In member function 'std::pair cytolib::CytoFrameView::get_range(const std::string&, cytolib::ColType, cytolib::RangeType) const': /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp:260:9: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 260 | { | ^ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -w -Wfatal-errors -I'/home/biocbuild/R/R-4.4.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c getPopStats.cpp -o getPopStats.o In file included from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:21, from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingSet.hpp:14, from getPopStats.cpp:1: /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp: In member function 'std::pair cytolib::CytoFrameView::get_range(const std::string&, cytolib::ColType, cytolib::RangeType) const': /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp:260:9: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 260 | { | ^ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -w -Wfatal-errors -I'/home/biocbuild/R/R-4.4.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c getSingleCellExpression.cpp -o getSingleCellExpression.o In file included from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:21, from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingSet.hpp:14, from getSingleCellExpression.cpp:1: /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp: In member function 'std::pair cytolib::CytoFrameView::get_range(const std::string&, cytolib::ColType, cytolib::RangeType) const': /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp:260:9: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 260 | { | ^ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -w -Wfatal-errors -I'/home/biocbuild/R/R-4.4.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c h5_error_r_handler.cpp -o h5_error_r_handler.o In file included from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:21, from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingSet.hpp:14, from ../inst/include/flowWorkspace/pairVectorCpp11Convert.h:12, from h5_error_r_handler.cpp:8: /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp: In member function 'std::pair cytolib::CytoFrameView::get_range(const std::string&, cytolib::ColType, cytolib::RangeType) const': /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp:260:9: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 260 | { | ^ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -w -Wfatal-errors -I'/home/biocbuild/R/R-4.4.1/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c setCounts.cpp -o setCounts.o In file included from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingHierarchy.hpp:21, from /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/GatingSet.hpp:14, from setCounts.cpp:1: /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp: In member function 'std::pair cytolib::CytoFrameView::get_range(const std::string&, cytolib::ColType, cytolib::RangeType) const': /home/biocbuild/R/R-4.4.1/site-library/cytolib/include/cytolib/CytoFrameView.hpp:260:9: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 260 | { | ^ g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o flowWorkspace.so R_API.o R_GatingHierarchy.o R_GatingSet.o cpp11.o cytoframeAPI.o cytosetAPI.o getDescendants.o getPopStats.o getSingleCellExpression.o h5_error_r_handler.o setCounts.o /home/biocbuild/R/R-4.4.1/site-library/cytolib/lib/libcytolib.a /home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/R/R-4.4.1/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -lopenblas -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-flowWorkspace/00new/flowWorkspace/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 (flowWorkspace)