############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL CytoML ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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 configure: CYTOLIBML_BIN=/usr/local/bin configure: creating ./config.status config.status: creating src/Makevars config.status: creating R/cytolibml_bin_path.R ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include' -I/usr/local/include -fpic -g -O2 -Wall -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] 435 | * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate | In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from /home/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ In file included from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17, from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14, from /home/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5, from ../inst/include/CytoML.h:4, from RcppExports.cpp:4: /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’: /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 58 | if(valVec.size() != 1+n+n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~ /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 62 | if(valVec.size() == 1+n+2*n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::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/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::flowJoWorkspace::get_sample_info(const std::vector >&, const CytoML::ParseWorkspaceParameters&)’: ../inst/include/CytoML/flowJoWorkspace.hpp:605:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 605 | for(int j = 0; j < sample_ids.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I'/home/biocbuild/bbs-3.14-bioc/R/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:9: ../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/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19, from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19, from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18, from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15, from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from /home/biocbuild/bbs-3.14-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: /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ In file included from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16, from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12, from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12, from /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14, from /home/biocbuild/bbs-3.14-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: /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’: /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 58 | if(valVec.size() != 1+n+n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~ /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 62 | if(valVec.size() == 1+n+2*n*n){ | ~~~~~~~~~~~~~~^~~~~~~~~~~~ /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::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/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::flowJoWorkspace::get_sample_info(const std::vector >&, const CytoML::ParseWorkspaceParameters&)’: ../inst/include/CytoML/flowJoWorkspace.hpp:605:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 605 | for(int j = 0; j < sample_ids.size(); j++) | ~~^~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o CytoML.so RcppExports.o parseFlowJoWorkspace.o /home/biocbuild/bbs-3.14-bioc/R/library/cytolib/lib/libcytolib.a /home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/lib/libsz.a -lcrypto -lcurl -lz -L/home/biocbuild/bbs-3.14-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.14-bioc/R/lib -lRblas -lxml2 -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.14-bioc/R/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)