* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’
* installing *source* package ‘COMIX’ ...
** this is package ‘COMIX’ version ‘1.0.0’
** package ‘COMIX’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Debian clang version 19.1.7 (3+b2)’
using C++11
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpIsu6Bz/R.INSTALL3ce900335fba9f/COMIX/src'
clang++-19 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppNumerical/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -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/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more. [-W#pragma-messages]
66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
| ^
In file included from RcppExports.cpp:5:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigenForward.h:29:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Sparse:26:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/SparseCore:61:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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:5:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigenForward.h:29:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Sparse:29:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/SparseLU:35:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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/tmp/R.check/r-devel-clang/Work/build/Packages/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:5:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigenForward.h:31:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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:5:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigenForward.h:37:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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;
| ^
6 warnings generated.
clang++-19 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppNumerical/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c armaMunkres.cpp -o armaMunkres.o
In file included from armaMunkres.cpp:1:
In file included from ./armaMunkres.h:3:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more. [-W#pragma-messages]
66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
| ^
1 warning generated.
clang++-19 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppNumerical/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c calibrateSN.cpp -o calibrateSN.o
In file included from calibrateSN.cpp:1:
In file included from ./perturbedSN_helpers.h:4:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more. [-W#pragma-messages]
66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
| ^
1 warning generated.
clang++-19 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppNumerical/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c main.cpp -o main.o
In file included from main.cpp:1:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more. [-W#pragma-messages]
66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
| ^
1 warning generated.
clang++-19 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppNumerical/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c perturbedSN_helpers.cpp -o perturbedSN_helpers.o
In file included from perturbedSN_helpers.cpp:1:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more. [-W#pragma-messages]
66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
| ^
In file included from perturbedSN_helpers.cpp:5:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppNumerical/include/RcppNumerical.h:10:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigenForward.h:29:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Sparse:26:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/SparseCore:61:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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 perturbedSN_helpers.cpp:5:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppNumerical/include/RcppNumerical.h:10:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigenForward.h:29:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Sparse:29:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/SparseLU:35:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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/tmp/R.check/r-devel-clang/Work/build/Packages/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 perturbedSN_helpers.cpp:5:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppNumerical/include/RcppNumerical.h:10:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigenForward.h:31:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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 perturbedSN_helpers.cpp:5:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppNumerical/include/RcppNumerical.h:10:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigenForward.h:37:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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;
| ^
6 warnings generated.
clang++-19 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppNumerical/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c perturbedSN_pmc.cpp -o perturbedSN_pmc.o
In file included from perturbedSN_pmc.cpp:1:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more. [-W#pragma-messages]
66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
| ^
1 warning generated.
clang++-19 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppNumerical/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -fpic -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -Wdeprecated-literal-operator -c relabel.cpp -o relabel.o
In file included from relabel.cpp:1:
In file included from ./armaMunkres.h:3:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more. [-W#pragma-messages]
66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
| ^
1 warning generated.
clang++-19 -std=gnu++11 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o COMIX.so RcppExports.o armaMunkres.o calibrateSN.o main.o perturbedSN_helpers.o perturbedSN_pmc.o relabel.o -fopenmp -llapack -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lRblas -L/usr/lib/llvm-19/lib -lFortranRuntime -lFortranDecimal -lm -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpIsu6Bz/R.INSTALL3ce900335fba9f/COMIX/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpIsu6Bz/R.INSTALL3ce900335fba9f/COMIX/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpIsu6Bz/R.INSTALL3ce900335fba9f/COMIX/src'
installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-COMIX/00new/COMIX/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 (COMIX)