* installing *source* package ‘lolog’ ...
** package ‘lolog’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 19.1.5’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/lolog/src'
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c RcppModule.cpp -o RcppModule.o
In file included from RcppModule.cpp:6:
In file included from ../inst/include/LatentOrderLikelihood.h:4:
In file included from ../inst/include/Model.h:6:
../inst/include/StatController.h:58:18: warning: instantiation of variable 'lolog::StatController<lolog::Undirected>::statMapPtr' required here, but no definition is available [-Wundefined-var-template]
58 | pS = statMapPtr->at(name);
| ^
../inst/include/Model.h:371:60: note: in instantiation of member function 'lolog::StatController<lolog::Undirected>::getStat' requested here
371 | AbstractStat<Engine>* ps = StatController<Engine>::getStat(name, params);
| ^
RcppModule.cpp:81:48: note: in instantiation of member function 'lolog::Model<lolog::Undirected>::addStatistic' requested here
81 | .method("addStatistic",&Model<Undirected>::addStatistic)
| ^
../inst/include/StatController.h:35:23: note: forward declaration of template entity is here
35 | static StatMapPtr statMapPtr;
| ^
../inst/include/StatController.h:58:18: note: add an explicit instantiation declaration to suppress this warning if 'lolog::StatController<lolog::Undirected>::statMapPtr' is explicitly instantiated in another translation unit
58 | pS = statMapPtr->at(name);
| ^
../inst/include/StatController.h:74:18: warning: instantiation of variable 'lolog::StatController<lolog::Undirected>::offsetMapPtr' required here, but no definition is available [-Wundefined-var-template]
74 | pS = offsetMapPtr->at(name);
| ^
../inst/include/Model.h:384:62: note: in instantiation of member function 'lolog::StatController<lolog::Undirected>::getOffset' requested here
384 | AbstractOffset<Engine>* ps = StatController<Engine>::getOffset(name, params);
| ^
RcppModule.cpp:82:45: note: in instantiation of member function 'lolog::Model<lolog::Undirected>::addOffset' requested here
82 | .method("addOffset",&Model<Undirected>::addOffset)
| ^
../inst/include/StatController.h:36:25: note: forward declaration of template entity is here
36 | static OffsetMapPtr offsetMapPtr;
| ^
../inst/include/StatController.h:74:18: note: add an explicit instantiation declaration to suppress this warning if 'lolog::StatController<lolog::Undirected>::offsetMapPtr' is explicitly instantiated in another translation unit
74 | pS = offsetMapPtr->at(name);
| ^
../inst/include/StatController.h:58:18: warning: instantiation of variable 'lolog::StatController<lolog::Directed>::statMapPtr' required here, but no definition is available [-Wundefined-var-template]
58 | pS = statMapPtr->at(name);
| ^
../inst/include/Model.h:371:60: note: in instantiation of member function 'lolog::StatController<lolog::Directed>::getStat' requested here
371 | AbstractStat<Engine>* ps = StatController<Engine>::getStat(name, params);
| ^
RcppModule.cpp:98:46: note: in instantiation of member function 'lolog::Model<lolog::Directed>::addStatistic' requested here
98 | .method("addStatistic",&Model<Directed>::addStatistic)
| ^
../inst/include/StatController.h:35:23: note: forward declaration of template entity is here
35 | static StatMapPtr statMapPtr;
| ^
../inst/include/StatController.h:58:18: note: add an explicit instantiation declaration to suppress this warning if 'lolog::StatController<lolog::Directed>::statMapPtr' is explicitly instantiated in another translation unit
58 | pS = statMapPtr->at(name);
| ^
../inst/include/StatController.h:74:18: warning: instantiation of variable 'lolog::StatController<lolog::Directed>::offsetMapPtr' required here, but no definition is available [-Wundefined-var-template]
74 | pS = offsetMapPtr->at(name);
| ^
../inst/include/Model.h:384:62: note: in instantiation of member function 'lolog::StatController<lolog::Directed>::getOffset' requested here
384 | AbstractOffset<Engine>* ps = StatController<Engine>::getOffset(name, params);
| ^
RcppModule.cpp:99:43: note: in instantiation of member function 'lolog::Model<lolog::Directed>::addOffset' requested here
99 | .method("addOffset",&Model<Directed>::addOffset)
| ^
../inst/include/StatController.h:36:25: note: forward declaration of template entity is here
36 | static OffsetMapPtr offsetMapPtr;
| ^
../inst/include/StatController.h:74:18: note: add an explicit instantiation declaration to suppress this warning if 'lolog::StatController<lolog::Directed>::offsetMapPtr' is explicitly instantiated in another translation unit
74 | pS = offsetMapPtr->at(name);
| ^
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c StatController.cpp -o StatController.o
In file included from StatController.cpp:3:
../inst/include/Stats.h:1173:16: warning: unused variable 'toDeg' [-Wunused-variable]
1173 | double toDeg;
| ^~~~~
../inst/include/Stats.h:1174:16: warning: unused variable 'fromDeg' [-Wunused-variable]
1174 | double fromDeg;
| ^~~~~~~
../inst/include/Stats.h:1185:16: warning: variable 'deg' set but not used [-Wunused-but-set-variable]
1185 | double deg = net.degree(from);
| ^
../inst/include/Stats.h:2450:16: warning: unused variable 'netSize' [-Wunused-variable]
2450 | double netSize = actorIndex + 1.0;
| ^~~~~~~
../inst/include/Stats.h:2451:16: warning: unused variable 'totDegree' [-Wunused-variable]
2451 | double totDegree = (net.nEdges() - hasEdge) * 2.0;
| ^~~~~~~~~
../inst/include/Stats.h:2457:16: warning: unused variable 'sdegs' [-Wunused-variable]
2457 | double sdegs = 0.0;
| ^~~~~
../inst/include/Stats.h:2791:12: warning: unused variable 'addingEdge' [-Wunused-variable]
2791 | bool addingEdge = !net.hasEdge(from,to);
| ^~~~~~~~~~
../inst/include/Stats.h:2976:10: warning: unused variable 'addingEdge' [-Wunused-variable]
2976 | bool addingEdge = !net.hasEdge(from,to);
| ^~~~~~~~~~
../inst/include/Stats.h:2458:26: warning: unused variable 'fit' [-Wunused-variable]
2458 | NeighborIterator fit = net.begin(order[actorIndex]);
| ^~~
../inst/include/Stat.h:247:14: note: in instantiation of member function 'lolog::SharedNbrs<lolog::Undirected>::dyadUpdate' requested here
247 | stat.dyadUpdate(net,from,to,order,actorIndex);
| ^
../inst/include/Stat.h:243:9: note: in instantiation of member function 'lolog::Stat<lolog::Undirected, lolog::SharedNbrs<lolog::Undirected>>::dyadUpdate' requested here
243 | dyadUpdate(net,from,to,order,actorIndex);
| ^
../inst/include/Stat.h:169:5: note: in instantiation of member function 'lolog::Stat<lolog::Undirected, lolog::SharedNbrs<lolog::Undirected>>::vDyadUpdate' requested here
169 | Stat() : stat(){}
| ^
StatController.cpp:86:42: note: in instantiation of member function 'lolog::Stat<lolog::Undirected, lolog::SharedNbrs<lolog::Undirected>>::Stat' requested here
86 | registerStatistic( UndirStatPtr( new UndirectedSharedNbrs() ) );
| ^
In file included from StatController.cpp:3:
../inst/include/Stats.h:2459:26: warning: unused variable 'fend' [-Wunused-variable]
2459 | NeighborIterator fend = net.end(order[actorIndex]);
| ^~~~
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c main.cpp -o main.o
4 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c test_BinaryNet.cpp -o test_BinaryNet.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c test_Constraints.cpp -o test_Constraints.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c test_LatentOrderLikelhood.cpp -o test_LatentOrderLikelhood.o
10 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c test_ParamParser.cpp -o test_ParamParser.o
In file included from test_Constraints.cpp:7:
../inst/include/Stats.h:1173:16: warning: unused variable 'toDeg' [-Wunused-variable]
1173 | double toDeg;
| ^~~~~
../inst/include/Stats.h:1174:16: warning: unused variable 'fromDeg' [-Wunused-variable]
1174 | double fromDeg;
| ^~~~~~~
../inst/include/Stats.h:1185:16: warning: variable 'deg' set but not used [-Wunused-but-set-variable]
1185 | double deg = net.degree(from);
| ^
../inst/include/Stats.h:2450:16: warning: unused variable 'netSize' [-Wunused-variable]
2450 | double netSize = actorIndex + 1.0;
| ^~~~~~~
../inst/include/Stats.h:2451:16: warning: unused variable 'totDegree' [-Wunused-variable]
2451 | double totDegree = (net.nEdges() - hasEdge) * 2.0;
| ^~~~~~~~~
../inst/include/Stats.h:2457:16: warning: unused variable 'sdegs' [-Wunused-variable]
2457 | double sdegs = 0.0;
| ^~~~~
../inst/include/Stats.h:2791:12: warning: unused variable 'addingEdge' [-Wunused-variable]
2791 | bool addingEdge = !net.hasEdge(from,to);
| ^~~~~~~~~~
../inst/include/Stats.h:2976:10: warning: unused variable 'addingEdge' [-Wunused-variable]
2976 | bool addingEdge = !net.hasEdge(from,to);
| ^~~~~~~~~~
In file included from test_LatentOrderLikelhood.cpp:5:
../inst/include/Stats.h:1173:16: warning: unused variable 'toDeg' [-Wunused-variable]
1173 | double toDeg;
| ^~~~~
../inst/include/Stats.h:1174:16: warning: unused variable 'fromDeg' [-Wunused-variable]
1174 | double fromDeg;
| ^~~~~~~
../inst/include/Stats.h:1185:16: warning: variable 'deg' set but not used [-Wunused-but-set-variable]
1185 | double deg = net.degree(from);
| ^
../inst/include/Stats.h:2450:16: warning: unused variable 'netSize' [-Wunused-variable]
2450 | double netSize = actorIndex + 1.0;
| ^~~~~~~
../inst/include/Stats.h:2451:16: warning: unused variable 'totDegree' [-Wunused-variable]
2451 | double totDegree = (net.nEdges() - hasEdge) * 2.0;
| ^~~~~~~~~
../inst/include/Stats.h:2457:16: warning: unused variable 'sdegs' [-Wunused-variable]
2457 | double sdegs = 0.0;
| ^~~~~
../inst/include/Stats.h:2791:12: warning: unused variable 'addingEdge' [-Wunused-variable]
2791 | bool addingEdge = !net.hasEdge(from,to);
| ^~~~~~~~~~
../inst/include/Stats.h:2976:10: warning: unused variable 'addingEdge' [-Wunused-variable]
2976 | bool addingEdge = !net.hasEdge(from,to);
| ^~~~~~~~~~
test_LatentOrderLikelhood.cpp:108:12: warning: unused variable 'llik' [-Wunused-variable]
108 | double llik = model.logLik();
| ^~~~
test_ParamParser.cpp:10:5: warning: unused label 'Rcpp' [-Wunused-label]
10 | Rcpp:List params = Rcpp::List::create(1, Rcpp::Named("a")=2, Rcpp::Named("b") = "ss");
| ^~~~~
8 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c test_Stats.cpp -o test_Stats.o
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c tests.cpp -o tests.o
In file included from test_Stats.cpp:4:
../inst/include/Stats.h:1173:16: warning: unused variable 'toDeg' [-Wunused-variable]
1173 | double toDeg;
| ^~~~~
../inst/include/Stats.h:1174:16: warning: unused variable 'fromDeg' [-Wunused-variable]
1174 | double fromDeg;
| ^~~~~~~
../inst/include/Stats.h:1185:16: warning: variable 'deg' set but not used [-Wunused-but-set-variable]
1185 | double deg = net.degree(from);
| ^
../inst/include/Stats.h:2450:16: warning: unused variable 'netSize' [-Wunused-variable]
2450 | double netSize = actorIndex + 1.0;
| ^~~~~~~
../inst/include/Stats.h:2451:16: warning: unused variable 'totDegree' [-Wunused-variable]
2451 | double totDegree = (net.nEdges() - hasEdge) * 2.0;
| ^~~~~~~~~
../inst/include/Stats.h:2457:16: warning: unused variable 'sdegs' [-Wunused-variable]
2457 | double sdegs = 0.0;
| ^~~~~
../inst/include/Stats.h:2791:12: warning: unused variable 'addingEdge' [-Wunused-variable]
2791 | bool addingEdge = !net.hasEdge(from,to);
| ^~~~~~~~~~
../inst/include/Stats.h:2976:10: warning: unused variable 'addingEdge' [-Wunused-variable]
2976 | bool addingEdge = !net.hasEdge(from,to);
| ^~~~~~~~~~
9 warnings generated.
8 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang19/lib -L/usr/local/clang19/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o lolog.so RcppExports.o RcppModule.o StatController.o main.o test_BinaryNet.o test_Constraints.o test_LatentOrderLikelhood.o test_ParamParser.o test_Stats.o tests.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/lolog/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/lolog/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/lolog/src'
installing to /data/gannet/ripley/R/packages/tests-clang/lolog.Rcheck/00LOCK-lolog/00new/lolog/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘[’ with signature ‘"Rcpp_DirectedNet"’: no definition for class “Rcpp_DirectedNet”
in method for ‘[’ with signature ‘"Rcpp_UndirectedNet"’: no definition for class “Rcpp_UndirectedNet”
in method for ‘[<-’ with signature ‘"Rcpp_DirectedNet"’: no definition for class “Rcpp_DirectedNet”
in method for ‘[<-’ with signature ‘"Rcpp_UndirectedNet"’: no definition for class “Rcpp_UndirectedNet”
** 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 (lolog)