* installing *source* package ‘modelSelection’ ...
** this is package ‘modelSelection’ version ‘1.0.3’
** package ‘modelSelection’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 21.1.1’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/modelSelection/src'
/usr/local/clang21/bin/clang++ -std=gnu++17 -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/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -DARMA_USE_OPENMP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c Polynomial.cpp -o Polynomial.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -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/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -DARMA_USE_OPENMP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c PolynomialRootFinder.cpp -o PolynomialRootFinder.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -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/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -DARMA_USE_OPENMP -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'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -DARMA_USE_OPENMP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c covariancemat.cpp -o covariancemat.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -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/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -DARMA_USE_OPENMP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c crossprodmat.cpp -o crossprodmat.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -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/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -DARMA_USE_OPENMP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c cstat.cpp -o cstat.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -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/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -DARMA_USE_OPENMP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c ggm.cpp -o ggm.o
In file included from ggm.cpp:1:
In file included from ./ggm.h:16:
In file included from ./modselIntegrals.h:8:
In file included from ./modelSel_regression.h:12:
In file included from ./glm.h:13:
./modselFunction.h:23:74: warning: struct 'lmObject' was previously declared as a class; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags]
23 | typedef void (*pt2hess)(double **H, double *th, int *sel, int *thlength, struct lmObject *, std::map<string, double*> *funargs);
| ^
./modselFunction.h:10:7: note: previous use is here
10 | class lmObject; //forward declaration (see modelSel_regression.h for actual declaration)
| ^
1 warning generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -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/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -DARMA_USE_OPENMP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c glm.cpp -o glm.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -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/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -DARMA_USE_OPENMP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c marginalLikelihood.cpp -o marginalLikelihood.o
In file included from glm.cpp:1:
In file included from ./glm.h:12:
In file included from ./modelSel_regression.h:13:
In file included from ./survival.h:14:
./modselFunction.h:23:74: warning: struct 'lmObject' was previously declared as a class; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags]
23 | typedef void (*pt2hess)(double **H, double *th, int *sel, int *thlength, struct lmObject *, std::map<string, double*> *funargs);
| ^
./modselFunction.h:10:7: note: previous use is here
10 | class lmObject; //forward declaration (see modelSel_regression.h for actual declaration)
| ^
1 warning generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -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/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -DARMA_USE_OPENMP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c mixtures.cpp -o mixtures.o
In file included from marginalLikelihood.cpp:13:
In file included from ./modelSel_regression.h:12:
In file included from ./glm.h:13:
./modselFunction.h:23:74: warning: struct 'lmObject' was previously declared as a class; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags]
23 | typedef void (*pt2hess)(double **H, double *th, int *sel, int *thlength, struct lmObject *, std::map<string, double*> *funargs);
| ^
./modselFunction.h:10:7: note: previous use is here
10 | class lmObject; //forward declaration (see modelSel_regression.h for actual declaration)
| ^
1 warning generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -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/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -DARMA_USE_OPENMP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c modelSel_regression.cpp -o modelSel_regression.o
In file included from modelSel_regression.cpp:13:
In file included from ./glm.h:12:
In file included from ./modelSel_regression.h:13:
In file included from ./survival.h:14:
./modselFunction.h:23:74: warning: struct 'lmObject' was previously declared as a class; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags]
23 | typedef void (*pt2hess)(double **H, double *th, int *sel, int *thlength, struct lmObject *, std::map<string, double*> *funargs);
| ^
./modselFunction.h:10:7: note: previous use is here
10 | class lmObject; //forward declaration (see modelSel_regression.h for actual declaration)
| ^
modelSel_regression.cpp:4257:65: warning: variable 'singlevarcount' set but not used [-Wunused-but-set-variable]
4257 | int i, j, i_var, j_var, varcount, groupcount, *groupsel, p_i, singlevarcount=0, npar= covariate_indexes->size();
| ^
modelSel_regression.cpp:6507:92: warning: variable 'y0Wsy0' set but not used [-Wunused-but-set-variable]
6507 | double sigma, alphat, alpha, w, w1, w2, ws1, ws2, wss1, wss2, *y0, *Wy0, *Wsy0, y0Wy0=0, y0Wsy0=0, y0Wssy0=0;
| ^
modelSel_regression.cpp:7928:44: warning: variable 'singlevarcount' set but not used [-Wunused-but-set-variable]
7928 | int i, *isgroup=lm->isgroup, varingroup, singlevarcount=0;
| ^
4 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -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/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -DARMA_USE_OPENMP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c modselFunction.cpp -o modselFunction.o
In file included from modselFunction.cpp:1:
./modselFunction.h:23:74: warning: struct 'lmObject' was previously declared as a class; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags]
23 | typedef void (*pt2hess)(double **H, double *th, int *sel, int *thlength, struct lmObject *, std::map<string, double*> *funargs);
| ^
./modselFunction.h:10:7: note: previous use is here
10 | class lmObject; //forward declaration (see modelSel_regression.h for actual declaration)
| ^
1 warning generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -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/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -DARMA_USE_OPENMP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c modselIntegrals.cpp -o modselIntegrals.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -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/clang21/include -I/usr/local/clang/include -fopenmp -DARMA_USE_CURRENT -DARMA_USE_OPENMP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c survival.cpp -o survival.o
In file included from modselIntegrals.cpp:1:
In file included from ./modselIntegrals.h:8:
In file included from ./modelSel_regression.h:12:
In file included from ./glm.h:13:
./modselFunction.h:23:74: warning: struct 'lmObject' was previously declared as a class; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags]
23 | typedef void (*pt2hess)(double **H, double *th, int *sel, int *thlength, struct lmObject *, std::map<string, double*> *funargs);
| ^
./modselFunction.h:10:7: note: previous use is here
10 | class lmObject; //forward declaration (see modelSel_regression.h for actual declaration)
| ^
1 warning generated.
In file included from survival.cpp:1:
In file included from ./survival.h:13:
In file included from ./modelSel_regression.h:12:
In file included from ./glm.h:13:
./modselFunction.h:23:74: warning: struct 'lmObject' was previously declared as a class; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags]
23 | typedef void (*pt2hess)(double **H, double *th, int *sel, int *thlength, struct lmObject *, std::map<string, double*> *funargs);
| ^
./modselFunction.h:10:7: note: previous use is here
10 | class lmObject; //forward declaration (see modelSel_regression.h for actual declaration)
| ^
survival.cpp:125:135: warning: variable 'sumD' set but not used [-Wunused-but-set-variable]
125 | double rho= th[*thlength -1], exprho, *y= (*lm).y, *x= (*lm).x, *ytXuncens= (*lm).ytXuncens, *res, *pnormres, ytres, *sumy2obs, *D, sumD=0, sumy2D=0, xyD, r;
| ^
survival.cpp:365:135: warning: variable 'sumD' set but not used [-Wunused-but-set-variable]
365 | double rho= th[*thlength -1], exprho, *y= (*lm).y, *x= (*lm).x, *ytXuncens= (*lm).ytXuncens, *res, *pnormres, ytres, *sumy2obs, *D, sumD=0, sumy2D=0, xyD, r;
| ^
3 warnings generated.
/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 -L/usr/local/clang21/lib/clang/21/lib/x86_64-unknown-linux-gnu -o modelSelection.so Polynomial.o PolynomialRootFinder.o RcppExports.o covariancemat.o crossprodmat.o cstat.o ggm.o glm.o marginalLikelihood.o mixtures.o modelSel_regression.o modselFunction.o modselIntegrals.o survival.o -fopenmp -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lflang_rt.runtime -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/modelSelection/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/modelSelection/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/modelSelection/src'
installing to /data/gannet/ripley/R/packages/tests-clang/modelSelection.Rcheck/00LOCK-modelSelection/00new/modelSelection/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (modelSelection)