* installing *source* package ‘glmmrBase’ ...
** this is package ‘glmmrBase’ version ‘1.0.0’
** using staged installation
Warning in .warning_nowrite(file.path(basename(pkgdir), ...)) :
  'glmmrBase/src/Makevars' already exists.  Not overwritten by rstantools.FALSE
Calls: <Anonymous> ... .setup_Makevars -> .add_stanfile -> .warning_nowrite
** libs
using C++ compiler: ‘Debian clang version 19.1.7 (3)’
using C++17


clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-19/include" -DNDEBUG -I"../inst/include" -I"/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0  -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I'/srv/hornik/tmp/CRAN_pretest/Library/SparseChol/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rstan/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/StanHeaders/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:29:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/Sparse:26:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/SparseCore:61:
/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  273 |       Index count = 0;
      |             ^
In file included from RcppExports.cpp:4:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:29:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/Sparse:29:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/SparseLU:35:
/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
   78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
      |         ^
/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
   79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
      |         ^
In file included from RcppExports.cpp:4:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:31:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
   72 |                         Index replacements = 0;
      |                               ^
In file included from RcppExports.cpp:4:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:37:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  246 |   int count = 0;
      |       ^
5 warnings generated.


clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-19/include" -DNDEBUG -I"../inst/include" -I"/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1 -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0  -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I'/srv/hornik/tmp/CRAN_pretest/Library/SparseChol/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/rstan/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/StanHeaders/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator  -c model_module.cpp -o model_module.o
In file included from model_module.cpp:1:
In file included from ../inst/include/glmmr.h:4:
In file included from ../inst/include/glmmr/general.h:10:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:29:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/Sparse:26:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/SparseCore:61:
/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  273 |       Index count = 0;
      |             ^
In file included from model_module.cpp:1:
In file included from ../inst/include/glmmr.h:4:
In file included from ../inst/include/glmmr/general.h:10:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:29:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/Sparse:29:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/SparseLU:35:
/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
   78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
      |         ^
/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
   79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
      |         ^
In file included from model_module.cpp:1:
In file included from ../inst/include/glmmr.h:4:
In file included from ../inst/include/glmmr/general.h:10:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:31:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
   72 |                         Index replacements = 0;
      |                               ^
In file included from model_module.cpp:1:
In file included from ../inst/include/glmmr.h:4:
In file included from ../inst/include/glmmr/general.h:10:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/RcppEigenForward.h:37:
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  246 |   int count = 0;
      |       ^
In file included from model_module.cpp:1:
In file included from ../inst/include/glmmr.h:4:
../inst/include/glmmr/general.h:21:9: warning: 'EIGEN_DEFAULT_DENSE_INDEX_TYPE' macro redefined [-Wmacro-redefined]
   21 | #define EIGEN_DEFAULT_DENSE_INDEX_TYPE int
      |         ^
/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include/Eigen/src/Core/util/Macros.h:33:9: note: previous definition is here
   33 | #define EIGEN_DEFAULT_DENSE_INDEX_TYPE std::ptrdiff_t
      |         ^
In file included from model_module.cpp:1:
In file included from ../inst/include/glmmr.h:4:
../inst/include/glmmr/general.h:39:10: fatal error: 'sparsechol.h' file not found
   39 | #include "sparsechol.h"
      |          ^~~~~~~~~~~~~~
6 warnings and 1 error generated.
make: *** [/home/hornik/tmp/R-d-clang-19/etc/Makeconf:209: model_module.o] Error 1
ERROR: compilation failed for package ‘glmmrBase’
* removing ‘/srv/hornik/tmp/CRAN_pretest/glmmrBase.Rcheck/glmmrBase’