* installing *source* package ‘greed’ ...
** package ‘greed’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 18.1.1’
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
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
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
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;
      |       ^
In file included from Gmm.cpp:5:
./Gmm.h:27:10: warning: private field 'normfact' is not used [-Wunused-private-field]
   27 |   double normfact;
      |          ^
1 warning 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
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 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
/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
/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
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;
      |              ^~
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;
      |              ^~
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 SimpleIclModel.cpp -o SimpleIclModel.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 SpMergeMat.cpp -o SpMergeMat.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 gicl_tools.cpp -o gicl_tools.o
SimpleIclCoModel.cpp:156:7: warning: unused variable 'cd' [-Wunused-variable]
  156 |   int cd = 0;
      |       ^~
1 warning generated.
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<arma::mat>(current1["S"]).n_cols, d=as<arma::mat>(current1["Yty"]).n_cols;
      |       ^
gicl_tools.cpp:765:10: warning: unused variable 'd' [-Wunused-variable]
  765 |   double d = m1.n_cols;
      |          ^
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)