* installing *source* package ‘greed’ ... ** package ‘greed’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘clang version 18.1.4’ using C++11 make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/greed/src' /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c CombinedIclModel.cpp -o CombinedIclModel.o /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c DcLbm.cpp -o DcLbm.o /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c DcSbm.cpp -o DcSbm.o /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c DcSbmUndirected.cpp -o DcSbmUndirected.o /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c DiagGmm.cpp -o DiagGmm.o /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Fit.cpp -o Fit.o /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Gmm.cpp -o Gmm.o /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c IclModel.cpp -o IclModel.o In file included from Gmm.cpp:5: ./Gmm.h:27:10: warning: private field 'normfact' is not used [-Wunused-private-field] 27 | double normfact; | ^ Fit.cpp:176:7: warning: unused variable 'N' [-Wunused-variable] 176 | int N = clr.n_elem; | ^ Fit.cpp:189:8: warning: variable 'M' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] 189 | if(model.is("DlvmPrior")){ | ^~~~~~~~~~~~~~~~~~~~~ Fit.cpp:207:10: note: uninitialized use occurs here 207 | return M; | ^ Fit.cpp:189:5: note: remove the 'if' if its condition is always true 189 | if(model.is("DlvmPrior")){ | ^~~~~~~~~~~~~~~~~~~~~~~~~ Fit.cpp:179:15: note: initialize the variable 'M' to silence this warning 179 | IclModel * M; | ^ | = nullptr /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Lca.cpp -o Lca.o 1 warning generated. IclModel.cpp:101:7: warning: variable 'nbmove' set but not used [-Wunused-but-set-variable] 101 | int nbmove = 0; | ^ IclModel.cpp:326:7: warning: variable 'nbmerge' set but not used [-Wunused-but-set-variable] 326 | int nbmerge = 0; | ^ IclModel.cpp:391:7: warning: variable 'nbmerge' set but not used [-Wunused-but-set-variable] 391 | int nbmerge = 0; | ^ IclModel.cpp:436:7: warning: variable 'nbmerge' set but not used [-Wunused-but-set-variable] 436 | int nbmerge = 0; | ^ 2 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c MergeMat.cpp -o MergeMat.o 4 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Mm.cpp -o Mm.o /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Mregs.cpp -o Mregs.o /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c MultSbm.cpp -o MultSbm.o /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c MultSbmUndirected.cpp -o MultSbmUndirected.o /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.o /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Sbm.cpp -o Sbm.o MultSbm.cpp:194:7: warning: unused variable 'cc' [-Wunused-variable] 194 | int cc, cc_old; | ^~ MultSbm.cpp:194:11: warning: unused variable 'cc_old' [-Wunused-variable] 194 | int cc, cc_old; | ^~~~~~ MultSbm.cpp:195:10: warning: unused variable 'oxc' [-Wunused-variable] 195 | double oxc,xc; | ^~~ MultSbm.cpp:195:14: warning: unused variable 'xc' [-Wunused-variable] 195 | double oxc,xc; | ^~ /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c SbmUndirected.cpp -o SbmUndirected.o MultSbmUndirected.cpp:33:7: warning: unused variable 'cc' [-Wunused-variable] 33 | int cc = 0; | ^~ MultSbmUndirected.cpp:72:7: warning: unused variable 'cc' [-Wunused-variable] 72 | int cc, cc_old; | ^~ MultSbmUndirected.cpp:72:11: warning: unused variable 'cc_old' [-Wunused-variable] 72 | int cc, cc_old; | ^~~~~~ MultSbmUndirected.cpp:73:10: warning: unused variable 'oxc' [-Wunused-variable] 73 | double oxc,xc; | ^~~ MultSbmUndirected.cpp:73:14: warning: unused variable 'xc' [-Wunused-variable] 73 | double oxc,xc; | ^~ 4 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c SimpleIclCoModel.cpp -o SimpleIclCoModel.o /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c SimpleIclModel.cpp -o SimpleIclModel.o /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c SpMergeMat.cpp -o SpMergeMat.o 5 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c gicl_tools.cpp -o gicl_tools.o SimpleIclCoModel.cpp:156:7: warning: unused variable 'cd' [-Wunused-variable] 156 | int cd = 0; | ^~ gicl_tools.cpp:420:21: warning: unused variable 'm' [-Wunused-variable] 420 | int n = X.n_rows, m = X.n_cols, d=Y.n_cols; | ^ gicl_tools.cpp:458:7: warning: unused variable 'm' [-Wunused-variable] 458 | int m = X.n_cols, d=Y.n_cols; | ^ gicl_tools.cpp:493:7: warning: unused variable 'm' [-Wunused-variable] 493 | int m = X.n_cols, d=Y.n_cols; | ^ gicl_tools.cpp:531:7: warning: unused variable 'm' [-Wunused-variable] 531 | int m = as(current1["S"]).n_cols, d=as(current1["Yty"]).n_cols; | ^ gicl_tools.cpp:765:10: warning: unused variable 'd' [-Wunused-variable] 765 | double d = m1.n_cols; | ^ 1 warning generated. 5 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++11 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o greed.so CombinedIclModel.o DcLbm.o DcSbm.o DcSbmUndirected.o DiagGmm.o Fit.o Gmm.o IclModel.o Lca.o MergeMat.o Mm.o Mregs.o MultSbm.o MultSbmUndirected.o RcppExports.o Sbm.o SbmUndirected.o SimpleIclCoModel.o SimpleIclModel.o SpMergeMat.o gicl_tools.o -fopenmp -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lFortran_main -lFortranRuntime -lFortranDecimal -lm make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/greed/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/greed/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/greed/src' installing to /data/gannet/ripley/R/packages/tests-clang/greed.Rcheck/00LOCK-greed/00new/greed/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘reorder’ in package ‘greed’ ** help *** installing help indices *** copying figures ** 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 (greed)