* installing *source* package ‘lolog’ ...
** this is package ‘lolog’ version ‘1.3.2’
** package ‘lolog’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 21.1.8’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/lolog/src'
/usr/local/clang21/bin/clang++ -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/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c RcppExports.cpp -o RcppExports.o
/usr/local/clang21/bin/clang++ -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/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -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);
| ^
4 warnings generated.
/usr/local/clang21/bin/clang++ -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/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c StatController.cpp -o StatController.o
In file included from StatController.cpp:3:
../inst/include/Stats.h:1187:16: warning: unused variable 'toDeg' [-Wunused-variable]
1187 | double toDeg;
| ^~~~~
../inst/include/Stats.h:1188:16: warning: unused variable 'fromDeg' [-Wunused-variable]
1188 | double fromDeg;
| ^~~~~~~
../inst/include/Stats.h:1199:16: warning: variable 'deg' set but not used [-Wunused-but-set-variable]
1199 | double deg = net.degree(from);
| ^
../inst/include/Stats.h:2464:16: warning: unused variable 'netSize' [-Wunused-variable]
2464 | double netSize = actorIndex + 1.0;
| ^~~~~~~
../inst/include/Stats.h:2465:16: warning: unused variable 'totDegree' [-Wunused-variable]
2465 | double totDegree = (net.nEdges() - hasEdge) * 2.0;
| ^~~~~~~~~
../inst/include/Stats.h:2471:16: warning: unused variable 'sdegs' [-Wunused-variable]
2471 | double sdegs = 0.0;
| ^~~~~
../inst/include/Stats.h:2805:12: warning: unused variable 'addingEdge' [-Wunused-variable]
2805 | bool addingEdge = !net.hasEdge(from,to);
| ^~~~~~~~~~
../inst/include/Stats.h:2990:10: warning: unused variable 'addingEdge' [-Wunused-variable]
2990 | bool addingEdge = !net.hasEdge(from,to);
| ^~~~~~~~~~
../inst/include/Stats.h:2472:26: warning: unused variable 'fit' [-Wunused-variable]
2472 | 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:87:42: note: in instantiation of member function 'lolog::Stat<lolog::Undirected, lolog::SharedNbrs<lolog::Undirected>>::Stat' requested here
87 | registerStatistic( UndirStatPtr( new UndirectedSharedNbrs() ) );
| ^
In file included from StatController.cpp:3:
../inst/include/Stats.h:2473:26: warning: unused variable 'fend' [-Wunused-variable]
2473 | NeighborIterator fend = net.end(order[actorIndex]);
| ^~~~
10 warnings generated.
/usr/local/clang21/bin/clang++ -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/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c main.cpp -o main.o
/usr/local/clang21/bin/clang++ -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/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c test_BinaryNet.cpp -o test_BinaryNet.o
/usr/local/clang21/bin/clang++ -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/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c test_Constraints.cpp -o test_Constraints.o
In file included from test_Constraints.cpp:7:
../inst/include/Stats.h:1187:16: warning: unused variable 'toDeg' [-Wunused-variable]
1187 | double toDeg;
| ^~~~~
../inst/include/Stats.h:1188:16: warning: unused variable 'fromDeg' [-Wunused-variable]
1188 | double fromDeg;
| ^~~~~~~
../inst/include/Stats.h:1199:16: warning: variable 'deg' set but not used [-Wunused-but-set-variable]
1199 | double deg = net.degree(from);
| ^
../inst/include/Stats.h:2464:16: warning: unused variable 'netSize' [-Wunused-variable]
2464 | double netSize = actorIndex + 1.0;
| ^~~~~~~
../inst/include/Stats.h:2465:16: warning: unused variable 'totDegree' [-Wunused-variable]
2465 | double totDegree = (net.nEdges() - hasEdge) * 2.0;
| ^~~~~~~~~
../inst/include/Stats.h:2471:16: warning: unused variable 'sdegs' [-Wunused-variable]
2471 | double sdegs = 0.0;
| ^~~~~
../inst/include/Stats.h:2805:12: warning: unused variable 'addingEdge' [-Wunused-variable]
2805 | bool addingEdge = !net.hasEdge(from,to);
| ^~~~~~~~~~
../inst/include/Stats.h:2990:10: warning: unused variable 'addingEdge' [-Wunused-variable]
2990 | bool addingEdge = !net.hasEdge(from,to);
| ^~~~~~~~~~
8 warnings generated.
/usr/local/clang21/bin/clang++ -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/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c test_LatentOrderLikelhood.cpp -o test_LatentOrderLikelhood.o
In file included from test_LatentOrderLikelhood.cpp:5:
../inst/include/Stats.h:1187:16: warning: unused variable 'toDeg' [-Wunused-variable]
1187 | double toDeg;
| ^~~~~
../inst/include/Stats.h:1188:16: warning: unused variable 'fromDeg' [-Wunused-variable]
1188 | double fromDeg;
| ^~~~~~~
../inst/include/Stats.h:1199:16: warning: variable 'deg' set but not used [-Wunused-but-set-variable]
1199 | double deg = net.degree(from);
| ^
../inst/include/Stats.h:2464:16: warning: unused variable 'netSize' [-Wunused-variable]
2464 | double netSize = actorIndex + 1.0;
| ^~~~~~~
../inst/include/Stats.h:2465:16: warning: unused variable 'totDegree' [-Wunused-variable]
2465 | double totDegree = (net.nEdges() - hasEdge) * 2.0;
| ^~~~~~~~~
../inst/include/Stats.h:2471:16: warning: unused variable 'sdegs' [-Wunused-variable]
2471 | double sdegs = 0.0;
| ^~~~~
../inst/include/Stats.h:2805:12: warning: unused variable 'addingEdge' [-Wunused-variable]
2805 | bool addingEdge = !net.hasEdge(from,to);
| ^~~~~~~~~~
../inst/include/Stats.h:2990:10: warning: unused variable 'addingEdge' [-Wunused-variable]
2990 | bool addingEdge = !net.hasEdge(from,to);
| ^~~~~~~~~~
test_LatentOrderLikelhood.cpp:108:12: warning: unused variable 'llik' [-Wunused-variable]
108 | double llik = model.logLik();
| ^~~~
9 warnings generated.
/usr/local/clang21/bin/clang++ -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/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c test_ParamParser.cpp -o test_ParamParser.o
/usr/local/clang21/bin/clang++ -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/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c test_Stats.cpp -o test_Stats.o
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");
| ^~~~~
In file included from test_Stats.cpp:4:
../inst/include/Stats.h:1187:16: warning: unused variable 'toDeg' [-Wunused-variable]
1187 | double toDeg;
| ^~~~~
../inst/include/Stats.h:1188:16: warning: unused variable 'fromDeg' [-Wunused-variable]
1188 | double fromDeg;
| ^~~~~~~
../inst/include/Stats.h:1199:16: warning: variable 'deg' set but not used [-Wunused-but-set-variable]
1199 | double deg = net.degree(from);
| ^
../inst/include/Stats.h:2464:16: warning: unused variable 'netSize' [-Wunused-variable]
2464 | double netSize = actorIndex + 1.0;
| ^~~~~~~
../inst/include/Stats.h:2465:16: warning: unused variable 'totDegree' [-Wunused-variable]
2465 | double totDegree = (net.nEdges() - hasEdge) * 2.0;
| ^~~~~~~~~
../inst/include/Stats.h:2471:16: warning: unused variable 'sdegs' [-Wunused-variable]
2471 | double sdegs = 0.0;
| ^~~~~
../inst/include/Stats.h:2805:12: warning: unused variable 'addingEdge' [-Wunused-variable]
2805 | bool addingEdge = !net.hasEdge(from,to);
| ^~~~~~~~~~
../inst/include/Stats.h:2990:10: warning: unused variable 'addingEdge' [-Wunused-variable]
2990 | bool addingEdge = !net.hasEdge(from,to);
| ^~~~~~~~~~
1 warning generated.
/usr/local/clang21/bin/clang++ -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/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c tests.cpp -o tests.o
8 warnings generated.
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
/usr/local/clang21/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang21/lib -L/usr/local/clang21/lib/x86_64-unknown-linux-gnu -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
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
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'
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
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)