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### Running command:
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### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL CytoML
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* 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_<Pred>::************
| ^
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::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::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::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::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::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::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::SampleInfo> CytoML::flowJoWorkspace::get_sample_info(const std::vector<int, std::allocator<int> >&, const CytoML::ParseWorkspaceParameters&)’:
../inst/include/CytoML/flowJoWorkspace.hpp:605:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::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_<Pred>::************
| ^
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::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::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::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::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::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::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::SampleInfo> CytoML::flowJoWorkspace::get_sample_info(const std::vector<int, std::allocator<int> >&, const CytoML::ParseWorkspaceParameters&)’:
../inst/include/CytoML/flowJoWorkspace.hpp:605:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::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)
